diff --git a/clang-tools-extra/clangd/IncludeCleaner.cpp b/clang-tools-extra/clangd/IncludeCleaner.cpp
--- a/clang-tools-extra/clangd/IncludeCleaner.cpp
+++ b/clang-tools-extra/clangd/IncludeCleaner.cpp
@@ -133,7 +133,7 @@
   void add(SourceLocation Loc) { add(SM.getFileID(Loc), Loc); }
 
   void add(FileID FID, SourceLocation Loc) {
-    if (FID.isInvalid())
+    if (FID.isInvalid() || SM.isWrittenInBuiltinFile(Loc))
       return;
     assert(SM.isInFileID(Loc, FID));
     if (Loc.isFileID()) {