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
@@ -129,7 +129,9 @@
   void add(SourceLocation Loc) { add(SM.getFileID(Loc), Loc); }
 
   void add(FileID FID, SourceLocation Loc) {
-    if (FID.isInvalid())
+    // Check if Loc is not written in a physical file.
+    if (FID.isInvalid() || SM.isWrittenInBuiltinFile(Loc) ||
+        SM.isWrittenInCommandLineFile(Loc))
       return;
     assert(SM.isInFileID(Loc, FID));
     if (Loc.isFileID()) {
diff --git a/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp b/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
--- a/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
+++ b/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
@@ -234,7 +234,7 @@
                                    "<system_header.h>"));
 }
 
-TEST(IncludeCleaner, ScratchBuffer) {
+TEST(IncludeCleaner, VirtualBuffers) {
   TestTU TU;
   TU.Filename = "foo.cpp";
   TU.Code = R"cpp(
@@ -242,6 +242,10 @@
 
     using flags::FLAGS_FOO;
 
+    // CLI will come from a define, __llvm__ is a built-in. In both cases, they
+    // come from non-existent files.
+    int y = CLI + __llvm__;
+
     int concat(a, b) = 42;
     )cpp";
   // The pasting operator in combination with DEFINE_FLAG will create
@@ -258,6 +262,7 @@
     #define ab x
     #define concat(x, y) x##y
     )cpp";
+  TU.ExtraArgs = {"-DCLI=42"};
   ParsedAST AST = TU.build();
   auto &SM = AST.getSourceManager();
   auto &Includes = AST.getIncludeStructure();