diff --git a/clang-tools-extra/clangd/SystemIncludeExtractor.cpp b/clang-tools-extra/clangd/SystemIncludeExtractor.cpp
--- a/clang-tools-extra/clangd/SystemIncludeExtractor.cpp
+++ b/clang-tools-extra/clangd/SystemIncludeExtractor.cpp
@@ -83,17 +83,16 @@
   // Whether certain includes should be part of query.
   bool StandardIncludes = true;
   bool StandardCXXIncludes = true;
-  bool BuiltinIncludes = true;
   // Language to use while querying.
   std::string Lang;
   std::string Sysroot;
   std::string ISysroot;
 
   bool operator==(const DriverArgs &RHS) const {
-    return std::tie(Driver, StandardIncludes, StandardCXXIncludes,
-                    BuiltinIncludes, Lang, Sysroot, ISysroot) ==
+    return std::tie(Driver, StandardIncludes, StandardCXXIncludes, Lang,
+                    Sysroot, ISysroot) ==
            std::tie(RHS.Driver, RHS.StandardIncludes, RHS.StandardCXXIncludes,
-                    RHS.BuiltinIncludes, RHS.Lang, RHS.Sysroot, ISysroot);
+                    RHS.Lang, RHS.Sysroot, ISysroot);
   }
 
   DriverArgs(const tooling::CompileCommand &Cmd, llvm::StringRef File) {
@@ -120,8 +119,6 @@
         StandardIncludes = false;
       else if (Arg == "-nostdinc++")
         StandardCXXIncludes = false;
-      else if (Arg == "-nobuiltininc")
-        BuiltinIncludes = false;
       // Figure out sysroot
       else if (Arg.consume_front("--sysroot")) {
         if (Arg.consume_front("="))
@@ -156,8 +153,6 @@
       Args.push_back("-nostdinc");
     if (!StandardCXXIncludes)
       Args.push_back("-nostdinc++");
-    if (!BuiltinIncludes)
-      Args.push_back("-nobuiltininc++");
     if (!Sysroot.empty())
       Args.append({"--sysroot", Sysroot});
     if (!ISysroot.empty())
@@ -190,7 +185,6 @@
         Val.Driver,
         Val.StandardIncludes,
         Val.StandardCXXIncludes,
-        Val.BuiltinIncludes,
         Val.Lang,
         Val.Sysroot,
         Val.ISysroot,
@@ -274,6 +268,42 @@
   return std::move(Info);
 }
 
+std::optional<std::string> run(llvm::ArrayRef<llvm::StringRef> Argv,
+                               bool OutputIsStderr) {
+  llvm::SmallString<128> OutputPath;
+  if (auto EC = llvm::sys::fs::createTemporaryFile("system-includes", "clangd",
+                                                   OutputPath)) {
+    elog("System include extraction: failed to create temporary file with "
+         "error {0}",
+         EC.message());
+    return std::nullopt;
+  }
+  auto CleanUp = llvm::make_scope_exit(
+      [&OutputPath]() { llvm::sys::fs::remove(OutputPath); });
+
+  std::optional<llvm::StringRef> Redirects[] = {{""}, {""}, {""}};
+  Redirects[OutputIsStderr ? 2 : 1] = OutputPath.str();
+
+  std::string ErrMsg;
+  if (int RC =
+          llvm::sys::ExecuteAndWait(Argv.front(), Argv, /*Env=*/std::nullopt,
+                                    Redirects, /*SecondsToWait=*/0,
+                                    /*MemoryLimit=*/0, &ErrMsg)) {
+    elog("System include extraction: driver execution failed with return code: "
+         "{0} - '{1}'. Args: [{2}]",
+         llvm::to_string(RC), ErrMsg, printArgv(Argv));
+    return std::nullopt;
+  }
+
+  auto BufOrError = llvm::MemoryBuffer::getFile(OutputPath);
+  if (!BufOrError) {
+    elog("System include extraction: failed to read {0} with error {1}",
+         OutputPath, BufOrError.getError().message());
+    return std::nullopt;
+  }
+  return BufOrError.get().get()->getBuffer().str();
+}
+
 std::optional<DriverInfo>
 extractSystemIncludesAndTarget(const DriverArgs &InputArgs,
                                const llvm::Regex &QueryDriverRegex) {
@@ -300,45 +330,37 @@
     return std::nullopt;
   }
 
-  llvm::SmallString<128> StdErrPath;
-  if (auto EC = llvm::sys::fs::createTemporaryFile("system-includes", "clangd",
-                                                   StdErrPath)) {
-    elog("System include extraction: failed to create temporary file with "
-         "error {0}",
-         EC.message());
-    return std::nullopt;
-  }
-  auto CleanUp = llvm::make_scope_exit(
-      [&StdErrPath]() { llvm::sys::fs::remove(StdErrPath); });
-
-  std::optional<llvm::StringRef> Redirects[] = {{""}, {""}, StdErrPath.str()};
-
   llvm::SmallVector<llvm::StringRef> Args = {Driver, "-E", "-v"};
   Args.append(InputArgs.render());
   // Input needs to go after Lang flags.
   Args.push_back("-");
-
-  std::string ErrMsg;
-  if (int RC = llvm::sys::ExecuteAndWait(Driver, Args, /*Env=*/std::nullopt,
-                                         Redirects, /*SecondsToWait=*/0,
-                                         /*MemoryLimit=*/0, &ErrMsg)) {
-    elog("System include extraction: driver execution failed with return code: "
-         "{0} - '{1}'. Args: [{2}]",
-         llvm::to_string(RC), ErrMsg, printArgv(Args));
+  auto Output = run(Args, /*OutputIsStderr=*/true);
+  if (!Output)
     return std::nullopt;
-  }
 
-  auto BufOrError = llvm::MemoryBuffer::getFile(StdErrPath);
-  if (!BufOrError) {
-    elog("System include extraction: failed to read {0} with error {1}",
-         StdErrPath, BufOrError.getError().message());
+  std::optional<DriverInfo> Info = parseDriverOutput(*Output);
+  if (!Info)
     return std::nullopt;
+
+  // The built-in headers are tightly coupled to parser builtins.
+  // (These are clang's "resource dir", GCC's GCC_INCLUDE_DIR.)
+  // We should keep using clangd's versions, so exclude the queried builtins.
+  // They're not specially marked in the -v output, but we can get the path
+  // with `$DRIVER -print-file-name=include`.
+  if (auto BuiltinHeaders =
+          run({Driver, "-print-file-name=include"}, /*OutputIsStderr=*/false)) {
+    auto Path = llvm::StringRef(*BuiltinHeaders).trim();
+    if (!Path.empty() && llvm::sys::path::is_absolute(Path)) {
+      auto Size = Info->SystemIncludes.size();
+      llvm::erase_if(Info->SystemIncludes,
+                     [&](llvm::StringRef Entry) { return Path == Entry; });
+      vlog("System includes extractor: builtin headers {0} {1}", Path,
+           (Info->SystemIncludes.size() != Size)
+               ? "excluded"
+               : "not found in driver's response");
+    }
   }
 
-  std::optional<DriverInfo> Info =
-      parseDriverOutput(BufOrError->get()->getBuffer());
-  if (!Info)
-    return std::nullopt;
   log("System includes extractor: successfully executed {0}\n\tgot includes: "
       "\"{1}\"\n\tgot target: \"{2}\"",
       Driver, llvm::join(Info->SystemIncludes, ", "), Info->Target);
diff --git a/clang-tools-extra/clangd/test/system-include-extractor.test b/clang-tools-extra/clangd/test/system-include-extractor.test
--- a/clang-tools-extra/clangd/test/system-include-extractor.test
+++ b/clang-tools-extra/clangd/test/system-include-extractor.test
@@ -10,6 +10,7 @@
 # %temp_dir%/my/dir2 as include search paths.
 # RUN: echo '#!/bin/sh' >> %t.dir/bin/my_driver.sh
 # RUN: echo '[ "$0" = "%t.dir/bin/my_driver.sh" ] || exit' >> %t.dir/bin/my_driver.sh
+# RUN: echo '[ "$1" = "-print-file-name=include" ] && echo "%t.dir/builtin" && exit' >> %t.dir/bin/my_driver.sh
 # RUN: echo 'args="$*"' >> %t.dir/bin/my_driver.sh
 # Check that clangd preserves certain flags like `-nostdinc` from
 # original invocation in compile_commands.json.
@@ -21,6 +22,7 @@
 # RUN: echo 'printf "#include <...> search starts here:\r\n" >&2' >> %t.dir/bin/my_driver.sh
 # RUN: echo 'echo %t.dir/my/dir/ >&2' >> %t.dir/bin/my_driver.sh
 # RUN: echo 'echo %t.dir/my/dir2/ >&2' >> %t.dir/bin/my_driver.sh
+# RUN: echo 'echo %t.dir/builtin >&2' >> %t.dir/bin/my_driver.sh
 # RUN: echo 'printf "End of search list.\r\n" >&2' >> %t.dir/bin/my_driver.sh
 # RUN: chmod +x %t.dir/bin/my_driver.sh
 
@@ -29,6 +31,8 @@
 # RUN: touch %t.dir/my/dir/a.h
 # RUN: mkdir -p %t.dir/my/dir2
 # RUN: touch %t.dir/my/dir2/b.h
+# RUN: mkdir -p %t.dir/builtin
+# RUN: touch %t.dir/builtin/c.h
 
 # Generate a compile_commands.json that will query the mock driver we've
 # created. Which should add a.h and b.h into include search path.
@@ -53,7 +57,7 @@
       "uri": "file://INPUT_DIR/the-file.cpp",
       "languageId":"cpp",
       "version":1,
-      "text":"#include <a.h>\n#include <b.h>\n#if !defined(__ARM_ARCH) || !defined(__gnu_linux__)\n#error \"Invalid target\"\n#endif\n"
+      "text":"#include <a.h>\n#include <b.h>\n#if !defined(__ARM_ARCH) || !defined(__gnu_linux__)\n#error \"Invalid target\"\n#endif\n#if __has_include(<c.h>)\n#error \"wrong-toolchain builtins\"\n#endif\n"
     }
   }
 }