diff --git a/clang-tools-extra/clangd/Headers.cpp b/clang-tools-extra/clangd/Headers.cpp
--- a/clang-tools-extra/clangd/Headers.cpp
+++ b/clang-tools-extra/clangd/Headers.cpp
@@ -10,6 +10,7 @@
 #include "Compiler.h"
 #include "SourceCode.h"
 #include "support/Logger.h"
+#include "clang/Basic/SourceLocation.h"
 #include "clang/Frontend/CompilerInstance.h"
 #include "clang/Frontend/CompilerInvocation.h"
 #include "clang/Frontend/FrontendActions.h"
@@ -30,12 +31,12 @@
   // in the main file are collected.
   void InclusionDirective(SourceLocation HashLoc, const Token &IncludeTok,
                           llvm::StringRef FileName, bool IsAngled,
-                          CharSourceRange FilenameRange, const FileEntry *File,
-                          llvm::StringRef /*SearchPath*/,
+                          CharSourceRange /*FilenameRange*/,
+                          const FileEntry *File, llvm::StringRef /*SearchPath*/,
                           llvm::StringRef /*RelativePath*/,
                           const Module * /*Imported*/,
                           SrcMgr::CharacteristicKind FileKind) override {
-    if (isInsideMainFile(HashLoc, SM)) {
+    auto AddMainFileInc = [&](SourceLocation HashLoc) {
       Out->MainFileIncludes.emplace_back();
       auto &Inc = Out->MainFileIncludes.back();
       Inc.Written =
@@ -47,22 +48,64 @@
           SM.getLineNumber(SM.getFileID(HashLoc), Inc.HashOffset) - 1;
       Inc.FileKind = FileKind;
       Inc.Directive = IncludeTok.getIdentifierInfo()->getPPKeywordID();
+    };
+
+    auto MainFID = SM.getMainFileID();
+    if (BuiltinFileInStack) {
+      // Directives included through builtin file can be mapped back to main
+      // file via line directives.
+      auto PreLoc = SM.getPresumedLoc(HashLoc);
+      if (auto FE = SM.getFileManager().getFile(PreLoc.getFilename())) {
+        if (SM.getFileEntryForID(MainFID) == *FE) {
+          HashLoc = SM.translateLineCol(MainFID, PreLoc.getLine(),
+                                        PreLoc.getColumn());
+          AddMainFileInc(HashLoc);
+        }
+      }
+    } else if (isInsideMainFile(HashLoc, SM)) {
+      AddMainFileInc(HashLoc);
     }
+
     if (File) {
       auto *IncludingFileEntry = SM.getFileEntryForID(SM.getFileID(HashLoc));
       if (!IncludingFileEntry) {
         assert(SM.getBufferName(HashLoc).startswith("<") &&
                "Expected #include location to be a file or <built-in>");
         // Treat as if included from the main file.
-        IncludingFileEntry = SM.getFileEntryForID(SM.getMainFileID());
+        IncludingFileEntry = SM.getFileEntryForID(MainFID);
       }
       Out->recordInclude(IncludingFileEntry->getName(), File->getName(),
                          File->tryGetRealPathName());
     }
   }
 
+  void FileChanged(SourceLocation Loc, FileChangeReason Reason,
+                   SrcMgr::CharacteristicKind FileType,
+                   FileID PrevFID) override {
+    switch (Reason) {
+    case PPCallbacks::EnterFile:
+      if (BuiltinFile.isInvalid() && SM.isWrittenInBuiltinFile(Loc)) {
+        BuiltinFile = SM.getFileID(Loc);
+        BuiltinFileInStack = true;
+      }
+      break;
+    case PPCallbacks::ExitFile:
+      if (PrevFID == BuiltinFile)
+        BuiltinFileInStack = false;
+      break;
+    case PPCallbacks::RenameFile:
+    case PPCallbacks::SystemHeaderPragma:
+      break;
+    }
+  }
+
 private:
   const SourceManager &SM;
+  // Set after entering the <built-in> file.
+  FileID BuiltinFile;
+  // Indicates whether <built-in> file is part of include stack.
+  bool BuiltinFileInStack = false;
+
   IncludeStructure *Out;
 };
 
diff --git a/clang-tools-extra/clangd/unittests/HeadersTests.cpp b/clang-tools-extra/clangd/unittests/HeadersTests.cpp
--- a/clang-tools-extra/clangd/unittests/HeadersTests.cpp
+++ b/clang-tools-extra/clangd/unittests/HeadersTests.cpp
@@ -16,6 +16,7 @@
 #include "clang/Frontend/CompilerInvocation.h"
 #include "clang/Frontend/FrontendActions.h"
 #include "clang/Lex/PreprocessorOptions.h"
+#include "llvm/Support/FormatVariadic.h"
 #include "llvm/Support/Path.h"
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
@@ -25,7 +26,9 @@
 namespace {
 
 using ::testing::AllOf;
+using ::testing::Contains;
 using ::testing::ElementsAre;
+using ::testing::Not;
 using ::testing::UnorderedElementsAre;
 
 class HeadersTest : public ::testing::Test {
@@ -302,6 +305,26 @@
             llvm::None);
 }
 
+TEST_F(HeadersTest, PresumedLocations) {
+  std::string HeaderFile = testPath("implicit_include.h");
+
+  // Line map inclusion back to main file.
+  std::string HeaderContents = llvm::formatv("#line 0 \"{0}\"", MainFile);
+  HeaderContents += R"cpp(
+#line 1
+#include <a.h>)cpp";
+  FS.Files[HeaderFile] = HeaderContents;
+
+  // Including through non-builtin file has no effects.
+  FS.Files[MainFile] = "#include \"implicit_include.h\"";
+  EXPECT_THAT(collectIncludes().MainFileIncludes,
+              Not(Contains(Written("<a.h>"))));
+
+  // Now include through built-in file.
+  CDB.ExtraClangFlags = {"-include" + HeaderFile};
+  EXPECT_THAT(collectIncludes().MainFileIncludes,
+              Contains(AllOf(IncludeLine(0), Written("<a.h>"))));
+}
 } // namespace
 } // namespace clangd
 } // namespace clang