diff --git a/.clangd b/.clangd
deleted file mode 100644
index c36b4792d750c..0000000000000
--- a/.clangd
+++ /dev/null
@@ -1,10 +0,0 @@
-# Used to allow clangd to run on CI platforms as part of //tools/clangd_check.
-#
-# Intended to have no effect elsewhere.
-#
-# See also:
-# - https://clangd.llvm.org/config#compileflags
-# - https://github.com/clangd/clangd/issues/662
-CompileFlags:
-  Add: -Wno-unknown-warning-option
-  Remove: [-m*, -f*]
diff --git a/ci/licenses_golden/licenses_flutter b/ci/licenses_golden/licenses_flutter
index 1f2f795bef59c..8cee3d263b758 100644
--- a/ci/licenses_golden/licenses_flutter
+++ b/ci/licenses_golden/licenses_flutter
@@ -45160,7 +45160,6 @@ ORIGIN: ../../../flutter/vulkan/vulkan_utilities.h + ../../../flutter/LICENSE
 ORIGIN: ../../../flutter/vulkan/vulkan_window.cc + ../../../flutter/LICENSE
 ORIGIN: ../../../flutter/vulkan/vulkan_window.h + ../../../flutter/LICENSE
 TYPE: LicenseType.bsd
-FILE: ../../../flutter/.clangd
 FILE: ../../../flutter/.engine-release.version
 FILE: ../../../flutter/.pylintrc
 FILE: ../../../flutter/assets/asset_manager.cc
diff --git a/tools/clangd_check/bin/main.dart b/tools/clangd_check/bin/main.dart
index d2e19dbb5c7dd..d5badb009dc34 100644
--- a/tools/clangd_check/bin/main.dart
+++ b/tools/clangd_check/bin/main.dart
@@ -106,8 +106,21 @@ void main(List<String> args) {
     return;
   }
 
-  // Run clangd.
+  final Engine engineRoot = Engine.findWithin(p.canonicalize(compileCommandsDir));
+  final io.File clangdConfig = io.File(p.join(engineRoot.flutterDir.path, '.clangd'));
   try {
+    // Write a .clangd file to the engine root directory.
+    //
+    // See:
+    // - https://clangd.llvm.org/config#compileflags
+    // - https://github.com/clangd/clangd/issues/662
+    clangdConfig.writeAsStringSync(
+      'CompileFlags:\n'
+      '  Add: -Wno-unknown-warning-option\n'
+      '  Remove: [-m*, -f*]\n'
+    );
+
+    // Run clangd.
     final io.ProcessResult result = io.Process.runSync(clangd, <String>[
       '--compile-commands-dir',
       compileCommandsDir,
@@ -128,5 +141,8 @@ void main(List<String> args) {
     io.stderr.writeln('Failed to run clangd: $e');
     io.stderr.writeln(const JsonEncoder.withIndent('  ').convert(entry));
     io.exitCode = 1;
+  } finally {
+    // Remove the copied .clangd file from the engine root directory.
+    clangdConfig.deleteSync();
   }
 }