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
@@ -121,7 +121,11 @@
     if (!Macros.insert(FID).second)
       return;
     const auto &Exp = SM.getSLocEntry(FID).getExpansion();
-    add(Exp.getSpellingLoc());
+    // For nested macro expansions, the spelling location can be within a
+    // temporary buffer that Clang creates (scratch space or ScratchBuffer).
+    // That is not a real file we can include.
+    if (!SM.isWrittenInScratchSpace(Exp.getSpellingLoc()))
+      add(Exp.getSpellingLoc());
     add(Exp.getExpansionLocStart());
     add(Exp.getExpansionLocEnd());
   }
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
@@ -167,6 +167,38 @@
               UnorderedElementsAre("\"unused.h\"", "\"dir/unused.h\""));
 }
 
+TEST(IncludeCleaner, ScratchBuffer) {
+  TestTU TU;
+  TU.Filename = "foo.cpp";
+  TU.Code = R"cpp(
+    #include "macro_spelling_in_scratch_buffer.h"
+
+    using flags::FLAGS_FOO;
+    )cpp";
+  // The pasting operator in combination with DEFINE_FLAG will create
+  // ScratchBuffer with `flags::FLAGS_FOO` that will have FileID but not
+  // FileEntry.
+  TU.AdditionalFiles["macro_spelling_in_scratch_buffer.h"] = R"cpp(
+    #define DEFINE_FLAG(X) \
+    namespace flags { \
+    int FLAGS_##X; \
+    } \
+
+    DEFINE_FLAG(FOO)
+    )cpp";
+  ParsedAST AST = TU.build();
+  auto &SM = AST.getSourceManager();
+  auto &Includes = AST.getIncludeStructure();
+  auto ReferencedFiles = translateToHeaderIDs(
+      findReferencedFiles(findReferencedLocations(AST), SM), Includes, SM);
+  auto Entry = SM.getFileManager().getFile(
+      testPath("macro_spelling_in_scratch_buffer.h"));
+  ASSERT_TRUE(Entry);
+  auto HeaderID = Includes.getID(*Entry);
+  EXPECT_THAT(ReferencedFiles, UnorderedElementsAre(HeaderID));
+  EXPECT_THAT(getUnused(Includes, ReferencedFiles), ::testing::IsEmpty());
+}
+
 } // namespace
 } // namespace clangd
 } // namespace clang