diff --git a/.ci/scripts/analyze_legacy.sh b/.ci/scripts/analyze_legacy.sh
index 391d520b4737..0a0ffcef5ea5 100755
--- a/.ci/scripts/analyze_legacy.sh
+++ b/.ci/scripts/analyze_legacy.sh
@@ -15,8 +15,7 @@ set -e
 # since only the packages changed by 'make-deps-path-based' need to be
 # re-checked.
 .ci/scripts/tool_runner.sh analyze --lib-only \
-    --skip-if-not-supporting-flutter-version="$CHANNEL" \
-    --custom-analysis=script/configs/custom_analysis.yaml
+    --skip-if-not-supporting-flutter-version="$CHANNEL"
 
 # Restore the tree to a clean state, to avoid accidental issues if
 # other script steps are added to the enclosing task.
diff --git a/.ci/scripts/analyze_pathified.sh b/.ci/scripts/analyze_pathified.sh
index 13939d8bd007..5cd98229d40a 100755
--- a/.ci/scripts/analyze_pathified.sh
+++ b/.ci/scripts/analyze_pathified.sh
@@ -17,7 +17,7 @@ set -e
 # failure regardless.
 dart ./script/tool/bin/flutter_plugin_tools.dart analyze --run-on-dirty-packages \
     --skip-if-resolving-fails \
-    --log-timing --custom-analysis=script/configs/custom_analysis.yaml
+    --log-timing
 # Restore the tree to a clean state, to avoid accidental issues if
 # other script steps are added to the enclosing task.
 git checkout .
diff --git a/.ci/targets/analyze.yaml b/.ci/targets/analyze.yaml
index 3d4f4716cff3..b2a393125b80 100644
--- a/.ci/targets/analyze.yaml
+++ b/.ci/targets/analyze.yaml
@@ -12,9 +12,7 @@ tasks:
     infra_step: true
   - name: analyze
     script: .ci/scripts/tool_runner.sh
-    # DO NOT change the custom-analysis argument here without changing the Dart repo.
-    # See the comment in script/configs/custom_analysis.yaml for details.
-    args: ["analyze", "--custom-analysis=script/configs/custom_analysis.yaml"]
+    args: ["analyze"]
     # Re-run analysis with path-based dependencies to ensure that publishing
     # the changes won't break analysis of other packages in the respository
     # that depend on it.
diff --git a/.ci/targets/analyze_downgraded.yaml b/.ci/targets/analyze_downgraded.yaml
index e4d1756665d4..2c0c46606364 100644
--- a/.ci/targets/analyze_downgraded.yaml
+++ b/.ci/targets/analyze_downgraded.yaml
@@ -7,4 +7,4 @@ tasks:
   # those APIs are introduced.
   - name: analyze - downgraded
     script: .ci/scripts/tool_runner.sh
-    args: ["analyze", "--downgrade", "--custom-analysis=script/configs/custom_analysis.yaml"]
+    args: ["analyze", "--downgrade"]
diff --git a/packages/animations/ci_config.yaml b/packages/animations/ci_config.yaml
new file mode 100644
index 000000000000..646cdfe9a3e2
--- /dev/null
+++ b/packages/animations/ci_config.yaml
@@ -0,0 +1,3 @@
+# Opts out of unawaited_futures, matching flutter/flutter's disabling due
+# to interactions with animation.
+allow_custom_analysis_options: true
diff --git a/packages/camera/camera_android_camerax/ci_config.yaml b/packages/camera/camera_android_camerax/ci_config.yaml
index c71f578cf0e6..4e65781cc456 100644
--- a/packages/camera/camera_android_camerax/ci_config.yaml
+++ b/packages/camera/camera_android_camerax/ci_config.yaml
@@ -1 +1,3 @@
 analyze_skills: true
+# Uses custom analysis to enable the cyclomatic complexity linter plugin.
+allow_custom_analysis_options: true
diff --git a/packages/cupertino_ui/ci_config.yaml b/packages/cupertino_ui/ci_config.yaml
index d3c078296f34..bcc591cbbd47 100644
--- a/packages/cupertino_ui/ci_config.yaml
+++ b/packages/cupertino_ui/ci_config.yaml
@@ -2,3 +2,7 @@
 exempt_from_excerpts: true
 release:
   batch: false
+
+# Temporarily ignore tests that have yet to have their cross imports fixed.
+# See https://github.com/flutter/flutter/issues/177028.
+allow_custom_analysis_options: true
diff --git a/packages/flutter_lints/ci_config.yaml b/packages/flutter_lints/ci_config.yaml
new file mode 100644
index 000000000000..64434b3e9556
--- /dev/null
+++ b/packages/flutter_lints/ci_config.yaml
@@ -0,0 +1,2 @@
+# Deliberately uses flutter_lints, as that's what it is demonstrating.
+allow_custom_analysis_options: true
diff --git a/packages/go_router/ci_config.yaml b/packages/go_router/ci_config.yaml
index 5784c6eb1d56..a9786cb5cf55 100644
--- a/packages/go_router/ci_config.yaml
+++ b/packages/go_router/ci_config.yaml
@@ -1,2 +1,6 @@
 release:
   batch: true
+
+# Has some test files that are intentionally broken to conduct dart fix tests.
+# Also opts out of unawaited_futures, matching flutter/flutter.
+allow_custom_analysis_options: true
diff --git a/packages/go_router_builder/ci_config.yaml b/packages/go_router_builder/ci_config.yaml
index f7160fb4571b..de0be5423080 100644
--- a/packages/go_router_builder/ci_config.yaml
+++ b/packages/go_router_builder/ci_config.yaml
@@ -1,3 +1,7 @@
 release:
   # TODO(chunhtai): Opt in when ready.
   batch: false
+
+# Uses default formatter settings instead of custom repo settings since it
+# serves as a golden for builder output tests.
+allow_custom_analysis_options: true
diff --git a/packages/material_ui/ci_config.yaml b/packages/material_ui/ci_config.yaml
index d3c078296f34..bcc591cbbd47 100644
--- a/packages/material_ui/ci_config.yaml
+++ b/packages/material_ui/ci_config.yaml
@@ -2,3 +2,7 @@
 exempt_from_excerpts: true
 release:
   batch: false
+
+# Temporarily ignore tests that have yet to have their cross imports fixed.
+# See https://github.com/flutter/flutter/issues/177028.
+allow_custom_analysis_options: true
diff --git a/packages/rfw/ci_config.yaml b/packages/rfw/ci_config.yaml
new file mode 100644
index 000000000000..d1cbe6ba2f2a
--- /dev/null
+++ b/packages/rfw/ci_config.yaml
@@ -0,0 +1,2 @@
+# Has some constructions that are currently handled poorly by dart format.
+allow_custom_analysis_options: true
diff --git a/packages/web_benchmarks/ci_config.yaml b/packages/web_benchmarks/ci_config.yaml
new file mode 100644
index 000000000000..c40b6aaf2a89
--- /dev/null
+++ b/packages/web_benchmarks/ci_config.yaml
@@ -0,0 +1,2 @@
+# Disables docs requirements, as it is test code.
+allow_custom_analysis_options: true
diff --git a/script/configs/custom_analysis.yaml b/script/configs/custom_analysis.yaml
deleted file mode 100644
index b4539c78a0e1..000000000000
--- a/script/configs/custom_analysis.yaml
+++ /dev/null
@@ -1,39 +0,0 @@
-# Packages that deliberately use their own analysis_options.yaml.
-#
-# Please consult with #hackers-ecosystem before adding anything to this list,
-# as the goal is to have consistent analysis options across all packages.
-#
-# All entries here shoud include a comment explaining why they use different
-# options.
-
-# DO NOT move or delete this file without updating
-# https://github.com/dart-lang/sdk/blob/main/tools/bots/flutter/analyze_flutter_packages.sh
-# and
-# https://github.com/flutter/flutter/blob/main/dev/bots/test.dart
-# which reference this file from source, but out-of-repo.
-# Contact stuartmorgan or devoncarew for assistance if necessary.
-
-# Opts out of unawaited_futures, matching flutter/flutter's disabling due
-# to interactions with animation.
-- animations
-# Temporarily ignore tests that have yet to have their cross imports fixed.
-# See https://github.com/flutter/flutter/issues/177028.
-- cupertino_ui
-# Deliberately uses flutter_lints, as that's what it is demonstrating.
-- flutter_lints/example
-# Has some test files that are intentionally broken to conduct dart fix tests.
-# Also opts out of unawaited_futures, matching flutter/flutter.
-- go_router
-# Uses default formatter settings instead of custom repo settings since it
-# serves as a golden for builder output tests.
-- go_router_builder/example
-# Temporarily ignore tests that have yet to have their cross imports fixed.
-# See https://github.com/flutter/flutter/issues/177028.
-- material_ui
-# Has some constructions that are currently handled poorly by dart format.
-- rfw/example
-# Disables docs requirements, as it is test code.
-- web_benchmarks/testing/test_app
-# Uses custom analysis to enable the cyclomatic complexity linter plugin.
-- camera/camera_android_camerax
-
diff --git a/script/tool/CHANGELOG.md b/script/tool/CHANGELOG.md
index 55aeacaf445b..aecc2e551d93 100644
--- a/script/tool/CHANGELOG.md
+++ b/script/tool/CHANGELOG.md
@@ -1,3 +1,9 @@
+## NEXT
+
+* Deprecates the `--custom-analysis` argument to `analyze`, which is now
+  ignored, in favor of `allow_custom_analysis_options: true` in package-level
+  `ci_config.yaml` files.
+
 ## 0.14.2
 
 * Ensures that pub commands use `flutter` or `dart` depending on whether the
diff --git a/script/tool/lib/src/analyze_command.dart b/script/tool/lib/src/analyze_command.dart
index 9db7abd6fb5d..b1363a646ee0 100644
--- a/script/tool/lib/src/analyze_command.dart
+++ b/script/tool/lib/src/analyze_command.dart
@@ -30,14 +30,12 @@ class AnalyzeCommand extends PackageLoopingCommand {
     argParser.addFlag(platformMacOS, help: "Runs 'xcodebuild analyze' on macOS code");
 
     // Dart options.
+    // TODO(stuartmorgan): Remove this entirely once the flutter/flutter and dart-lang repo scripts
+    // that run flutter/packages analysis have been updated not to pass it.
     argParser.addMultiOption(
-      _customAnalysisFlag,
-      help:
-          'Directories (comma separated) that are allowed to have their own '
-          'analysis options.\n\n'
-          'Alternately, a list of one or more YAML files that contain a list '
-          'of allowed directories.',
-      defaultsTo: <String>[],
+      'custom-analysis',
+      help: 'Ignored; exists for legacy compatibility only.',
+      hide: true,
     );
     argParser.addOption(
       _analysisSdk,
@@ -85,7 +83,6 @@ class AnalyzeCommand extends PackageLoopingCommand {
   }
 
   static const String _dartFlag = 'dart';
-  static const String _customAnalysisFlag = 'custom-analysis';
   static const String _downgradeFlag = 'downgrade';
   static const String _libOnlyFlag = 'lib-only';
   static const String _analysisSdk = 'analysis-sdk';
@@ -95,8 +92,6 @@ class AnalyzeCommand extends PackageLoopingCommand {
 
   late String _dartBinaryPath;
 
-  Set<String> _allowedCustomAnalysisDirectories = const <String>{};
-
   @override
   final String name = 'analyze';
 
@@ -105,8 +100,8 @@ class AnalyzeCommand extends PackageLoopingCommand {
       'Analyzes all packages using dart analyze.\n\n'
       'This command requires "dart" and "flutter" to be in your path.';
 
-  /// Checks that there are no unexpected analysis_options.yaml files.
-  bool _hasUnexpectedAnalysisOptions(RepositoryPackage package) {
+  /// Checks that there are no package-local analysis_options.yaml files.
+  bool _hasLocalAnalysisOptions(RepositoryPackage package) {
     final List<FileSystemEntity> files = package.directory.listSync(
       recursive: true,
       followLinks: false,
@@ -121,19 +116,12 @@ class AnalyzeCommand extends PackageLoopingCommand {
         continue;
       }
 
-      final bool allowed = _allowedCustomAnalysisDirectories.any(
-        (String directory) =>
-            directory.isNotEmpty &&
-            path.isWithin(packagesDir.childDirectory(directory).path, file.path),
-      );
-      if (allowed) {
-        continue;
-      }
-
-      printError('Found an extra analysis_options.yaml at ${file.absolute.path}.');
+      printError('Found an unexpected analysis_options.yaml at ${file.absolute.path}.');
       printError(
-        'If this was deliberate, pass the package to the analyze command '
-        'with the --$_customAnalysisFlag flag and try again.',
+        'If this is an intentional exception to the general repository guidance against having '
+        'custom analysis_options.yaml files, add a ci_config.yaml to this package that '
+        'sets "allow_custom_analysis_options: true", with a comment explaining why an exception '
+        'is needed.',
       );
       return true;
     }
@@ -170,8 +158,6 @@ class AnalyzeCommand extends PackageLoopingCommand {
 
   @override
   Future<void> initializeRun() async {
-    _allowedCustomAnalysisDirectories = getYamlListArg(_customAnalysisFlag);
-
     // Use the Dart SDK override if one was passed in.
     final dartSdk = argResults![_analysisSdk] as String?;
     _dartBinaryPath = dartSdk == null ? 'dart' : path.join(dartSdk, 'bin', 'dart');
@@ -303,7 +289,10 @@ class AnalyzeCommand extends PackageLoopingCommand {
       }
     }
 
-    if (_hasUnexpectedAnalysisOptions(package)) {
+    // Require an explicit opt-in to use custom analysis options, since it's very easy to
+    // accidentally introduce them to the repo (e.g., with 'flutter create').
+    if (!(package.parseCIConfig()?.allowCustomAnalysisOptions ?? false) &&
+        _hasLocalAnalysisOptions(package)) {
       return PackageResult.fail(<String>['Unexpected local analysis options']);
     }
     final int mainExitCode = await processRunner.runAndStream(_dartBinaryPath, <String>[
diff --git a/script/tool/lib/src/common/ci_config.dart b/script/tool/lib/src/common/ci_config.dart
index f7c9ca34e641..8c2a368443ba 100644
--- a/script/tool/lib/src/common/ci_config.dart
+++ b/script/tool/lib/src/common/ci_config.dart
@@ -4,6 +4,12 @@
 
 import 'package:yaml/yaml.dart';
 
+const String _releaseModeKey = 'release';
+const String _isBatchModeKey = 'batch';
+const String _exemptFromExcerptsKey = 'exempt_from_excerpts';
+const String _analyzeSkillsKey = 'analyze_skills';
+const String _allowCustomAnalysisOptionsKey = 'allow_custom_analysis_options';
+
 /// A class representing the parsed content of a `ci_config.yaml` file.
 class CIConfig {
   /// Creates a [CIConfig] from a parsed YAML map.
@@ -11,6 +17,7 @@ class CIConfig {
     required this.isBatchRelease,
     required this.requiresExcerpts,
     required this.analyzeSkills,
+    required this.allowCustomAnalysisOptions,
   });
 
   /// Parses a [CIConfig] from a YAML string.
@@ -25,30 +32,34 @@ class CIConfig {
     _checkCIConfigEntries(loaded, syntax: _validCIConfigSyntax);
 
     var isBatchRelease = false;
-    final Object? release = loaded['release'];
+    final Object? release = loaded[_releaseModeKey];
     if (release is Map) {
-      isBatchRelease = release['batch'] == true;
+      isBatchRelease = release[_isBatchModeKey] == true;
     }
 
     // Any package that hasn't been explicitly exempted is assumed to require
     // excerpts.
-    final requiresExcerpts = loaded['exempt_from_excerpts'] != true;
+    final requiresExcerpts = loaded[_exemptFromExcerptsKey] != true;
+
+    final analyzeSkills = loaded[_analyzeSkillsKey] == true;
 
-    final analyzeSkills = loaded['analyze_skills'] == true;
+    final allowCustomAnalysisOptions = loaded[_allowCustomAnalysisOptionsKey] == true;
 
     return CIConfig._(
       isBatchRelease: isBatchRelease,
       requiresExcerpts: requiresExcerpts,
       analyzeSkills: analyzeSkills,
+      allowCustomAnalysisOptions: allowCustomAnalysisOptions,
     );
   }
 
   static const Map<String, Object?> _validCIConfigSyntax = <String, Object?>{
-    'release': <String, Object?>{
-      'batch': <bool>{true, false},
+    _releaseModeKey: <String, Object?>{
+      _isBatchModeKey: <bool>{true, false},
     },
-    'exempt_from_excerpts': <bool>{true, false},
-    'analyze_skills': <bool>{true, false},
+    _exemptFromExcerptsKey: <bool>{true, false},
+    _analyzeSkillsKey: <bool>{true, false},
+    _allowCustomAnalysisOptionsKey: <bool>{true, false},
   };
 
   /// Returns true if the package is configured for batch release.
@@ -60,6 +71,9 @@ class CIConfig {
   /// Returns true if the package has its agent skills analyzed.
   final bool analyzeSkills;
 
+  /// Returns true if the package is allowed to have its own analysis options.
+  final bool allowCustomAnalysisOptions;
+
   static void _checkCIConfigEntries(
     YamlMap config, {
     required Map<String, Object?> syntax,
diff --git a/script/tool/test/analyze_command_test.dart b/script/tool/test/analyze_command_test.dart
index 57124c2ebaa5..6f1dacbbac26 100644
--- a/script/tool/test/analyze_command_test.dart
+++ b/script/tool/test/analyze_command_test.dart
@@ -315,7 +315,7 @@ void main() {
     });
 
     group('verifies analysis settings', () {
-      test('fails analysis_options.yaml', () async {
+      test('fails for unexpected analysis_options.yaml', () async {
         createFakePlugin('foo', packagesDir, extraFiles: <String>['analysis_options.yaml']);
 
         Error? commandError;
@@ -331,7 +331,9 @@ void main() {
         expect(
           output,
           containsAllInOrder(<Matcher>[
-            contains('Found an extra analysis_options.yaml at /packages/foo/analysis_options.yaml'),
+            contains(
+              'Found an unexpected analysis_options.yaml at /packages/foo/analysis_options.yaml',
+            ),
             contains(
               '  foo:\n'
               '    Unexpected local analysis options',
@@ -340,7 +342,7 @@ void main() {
         );
       });
 
-      test('fails .analysis_options', () async {
+      test('fails on .analysis_options', () async {
         createFakePlugin('foo', packagesDir, extraFiles: <String>['.analysis_options']);
 
         Error? commandError;
@@ -356,7 +358,9 @@ void main() {
         expect(
           output,
           containsAllInOrder(<Matcher>[
-            contains('Found an extra analysis_options.yaml at /packages/foo/.analysis_options'),
+            contains(
+              'Found an unexpected analysis_options.yaml at /packages/foo/.analysis_options',
+            ),
             contains(
               '  foo:\n'
               '    Unexpected local analysis options',
@@ -365,30 +369,13 @@ void main() {
         );
       });
 
-      test('takes an allow list', () async {
-        final RepositoryPackage plugin = createFakePlugin(
-          'foo',
-          packagesDir,
-          extraFiles: <String>['analysis_options.yaml'],
-        );
-
-        await runCapturingPrint(runner, <String>['analyze', '--custom-analysis', 'foo']);
-
-        expect(
-          processRunner.recordedCalls,
-          orderedEquals(<ProcessCall>[
-            ProcessCall('flutter', const <String>['pub', 'get'], plugin.path),
-            ProcessCall('dart', const <String>['analyze', '--fatal-infos'], plugin.path),
-          ]),
-        );
-      });
-
       test('ignores analysis options in the plugin .symlinks directory', () async {
         final RepositoryPackage plugin = createFakePlugin(
           'foo',
           packagesDir,
           extraFiles: <String>['analysis_options.yaml'],
         );
+        plugin.ciConfigFile.writeAsStringSync('allow_custom_analysis_options: true');
         final RepositoryPackage includingPackage = createFakePlugin('bar', packagesDir);
         // Simulate the local state of having built 'bar' if it includes 'foo'.
         includingPackage.directory
@@ -397,19 +384,18 @@ void main() {
             .childLink('.symlinks')
             .createSync(plugin.directory.path, recursive: true);
 
-        await runCapturingPrint(runner, <String>['analyze', '--custom-analysis', 'foo']);
+        await runCapturingPrint(runner, <String>['analyze']);
       });
 
-      test('takes an allow config file', () async {
+      test('allows analysis options when configured', () async {
         final RepositoryPackage plugin = createFakePlugin(
           'foo',
           packagesDir,
           extraFiles: <String>['analysis_options.yaml'],
         );
-        final File allowFile = packagesDir.childFile('custom.yaml');
-        allowFile.writeAsStringSync('- foo');
+        plugin.ciConfigFile.writeAsStringSync('allow_custom_analysis_options: true');
 
-        await runCapturingPrint(runner, <String>['analyze', '--custom-analysis', allowFile.path]);
+        await runCapturingPrint(runner, <String>['analyze']);
 
         expect(
           processRunner.recordedCalls,
@@ -419,27 +405,6 @@ void main() {
           ]),
         );
       });
-
-      test('allows an empty config file', () async {
-        createFakePlugin('foo', packagesDir, extraFiles: <String>['analysis_options.yaml']);
-        final File allowFile = packagesDir.childFile('custom.yaml');
-        allowFile.createSync();
-
-        await expectLater(
-          () => runCapturingPrint(runner, <String>['analyze', '--custom-analysis', allowFile.path]),
-          throwsA(isA<ToolExit>()),
-        );
-      });
-
-      // See: https://github.com/flutter/flutter/issues/78994
-      test('takes an empty allow list', () async {
-        createFakePlugin('foo', packagesDir, extraFiles: <String>['analysis_options.yaml']);
-
-        await expectLater(
-          () => runCapturingPrint(runner, <String>['analyze', '--custom-analysis', '']),
-          throwsA(isA<ToolExit>()),
-        );
-      });
     });
 
     group('dart_code_linter', () {
@@ -654,6 +619,7 @@ void main() {
           isFlutter: true,
         );
         _writeFakePubspecWithLinter(package, inDevDependencies: true);
+        package.ciConfigFile.writeAsStringSync('allow_custom_analysis_options: true');
         package.directory.childFile('analysis_options.yaml').writeAsStringSync('''
 dart_code_linter:
   metrics:
@@ -670,7 +636,7 @@ dart_code_linter:
         Error? commandError;
         final List<String> output = await runCapturingPrint(
           runner,
-          <String>['analyze', '--custom-analysis', 'a_package'],
+          <String>['analyze'],
           errorHandler: (Error e) {
             commandError = e;
           },
@@ -830,7 +796,7 @@ dart_code_linter:
           Error? commandError;
           final List<String> output = await runCapturingPrint(
             runner,
-            <String>['analyze', '--custom-analysis', 'a_package'],
+            <String>['analyze'],
             errorHandler: (Error e) {
               commandError = e;
             },
@@ -966,13 +932,10 @@ dart_code_linter:
     // modify the script above, as it is run from source, but out-of-repo.
     // Contact stuartmorgan or devoncarew for assistance.
     test('Dart repo analyze command works', () async {
-      final RepositoryPackage plugin = createFakePlugin(
-        'foo',
-        packagesDir,
-        extraFiles: <String>['analysis_options.yaml'],
-      );
+      final RepositoryPackage plugin = createFakePlugin('foo', packagesDir);
       final File allowFile = packagesDir.childFile('custom.yaml');
-      allowFile.writeAsStringSync('- foo');
+      // Intentionally do not create the file; this ensures that removing the legacy file from this
+      // repository won't break the other callers.
 
       await runCapturingPrint(runner, <String>[
         // DO NOT change this call; see comment above.