diff --git a/DEPS b/DEPS
index 7996f13867..589686e683 100644
--- a/DEPS
+++ b/DEPS
@@ -637,7 +637,7 @@ deps = {
     ],
     'dep_type': 'cipd',
   },
-  'engine/src/flutter/third_party/ninja': {
+  'third_party/ninja': {
     'packages': [
       {
         'package': 'infra/3pp/tools/ninja/${{platform}}',
diff --git a/buildtools/README.md b/buildtools/README.md
new file mode 100644
index 0000000000..3d0b26bc8e
--- /dev/null
+++ b/buildtools/README.md
@@ -0,0 +1 @@
+This directory is a placeholder intended to make Flutter's source tree match the expectations of [depot_tools](https://www.chromium.org/developers/how-tos/depottools/), which is used to build the Flutter engine.
diff --git a/dev/bots/analyze.dart b/dev/bots/analyze.dart
index eca1f1e98c..b46863f43d 100644
--- a/dev/bots/analyze.dart
+++ b/dev/bots/analyze.dart
@@ -1632,6 +1632,7 @@ Future<void> verifyRepositoryLinks(String workingDirectory) async {
     'glfw/glfw',
     'GoogleCloudPlatform/artifact-registry-maven-tools',
     'material-components/material-components-android', // TODO(guidezpl): remove when https://github.com/material-components/material-components-android/issues/4144 is closed
+    'ninja-build/ninja',
     'torvalds/linux',
     'tpn/winsdk-10',
   };
diff --git a/engine/src/flutter/ci/licenses_golden/excluded_files b/engine/src/flutter/ci/licenses_golden/excluded_files
index 4656ce3d33..88cb1dd294 100644
--- a/engine/src/flutter/ci/licenses_golden/excluded_files
+++ b/engine/src/flutter/ci/licenses_golden/excluded_files
@@ -2295,7 +2295,6 @@
 ../../../flutter/third_party/libwebp/swig
 ../../../flutter/third_party/libwebp/tests
 ../../../flutter/third_party/libwebp/webp_js
-../../../flutter/third_party/ninja
 ../../../flutter/third_party/ocmock
 ../../../flutter/third_party/perfetto/.clang-format
 ../../../flutter/third_party/perfetto/.clang-tidy
diff --git a/engine/src/flutter/tools/pkg/engine_build_configs/lib/src/build_config_runner.dart b/engine/src/flutter/tools/pkg/engine_build_configs/lib/src/build_config_runner.dart
index cbf155a699..b021fa115d 100644
--- a/engine/src/flutter/tools/pkg/engine_build_configs/lib/src/build_config_runner.dart
+++ b/engine/src/flutter/tools/pkg/engine_build_configs/lib/src/build_config_runner.dart
@@ -583,8 +583,7 @@ final class BuildRunner extends Runner {
     bool success = false;
     try {
       final String ninjaPath = p.join(
-        engineSrcDir.path,
-        'flutter',
+        engineSrcDir.parent.parent.path,
         'third_party',
         'ninja',
         'ninja',
diff --git a/engine/src/flutter/tools/pkg/engine_build_configs/test/build_config_runner_test.dart b/engine/src/flutter/tools/pkg/engine_build_configs/test/build_config_runner_test.dart
index 8131293816..0fdc588745 100644
--- a/engine/src/flutter/tools/pkg/engine_build_configs/test/build_config_runner_test.dart
+++ b/engine/src/flutter/tools/pkg/engine_build_configs/test/build_config_runner_test.dart
@@ -116,7 +116,8 @@ void main() {
     // Check that the events for the Ninja command are correct.
     expect(events[2] is RunnerStart, isTrue);
     expect(events[2].name, equals('$buildName: ninja'));
-    expect(events[2].command[0], contains('ninja'));
+    final String rootPath = path.dirname(path.dirname(engine.srcDir.path));
+    expect(events[2].command[0], equals('$rootPath/third_party/ninja/ninja'));
     final String configPath = '${engine.srcDir.path}/out/${targetBuild.ninja.config}';
     expect(events[2].command.contains(configPath), isTrue);
     for (final String target in targetBuild.ninja.targets) {
diff --git a/third_party/.gitignore b/third_party/.gitignore
new file mode 100644
index 0000000000..b528e9e24b
--- /dev/null
+++ b/third_party/.gitignore
@@ -0,0 +1,9 @@
+# Ignore everything by default, as these come from gclient/DEPS.
+# We'll explicitly include the folders we want to track.
+/*
+
+# Include the .gitignore file itself.
+!.gitignore
+
+# Allow custom README.flutter files in each folder.
+**/README.flutter
diff --git a/engine/src/flutter/third_party/ninja/README.flutter b/third_party/ninja/README.flutter
similarity index 100%
rename from engine/src/flutter/third_party/ninja/README.flutter
rename to third_party/ninja/README.flutter