diff --git a/clang-tools-extra/clangd/Diagnostics.h b/clang-tools-extra/clangd/Diagnostics.h
--- a/clang-tools-extra/clangd/Diagnostics.h
+++ b/clang-tools-extra/clangd/Diagnostics.h
@@ -180,7 +180,8 @@
 
 /// Determine whether a (non-clang-tidy) diagnostic is suppressed by config.
 bool isBuiltinDiagnosticSuppressed(unsigned ID,
-                                   const llvm::StringSet<> &Suppressed);
+                                   const llvm::StringSet<> &Suppressed,
+                                   const LangOptions &);
 /// Take a user-specified diagnostic code, and convert it to a normalized form
 /// stored in the config and consumed by isBuiltinDiagnosticsSuppressed.
 ///
diff --git a/clang-tools-extra/clangd/Diagnostics.cpp b/clang-tools-extra/clangd/Diagnostics.cpp
--- a/clang-tools-extra/clangd/Diagnostics.cpp
+++ b/clang-tools-extra/clangd/Diagnostics.cpp
@@ -879,7 +879,14 @@
 }
 
 bool isBuiltinDiagnosticSuppressed(unsigned ID,
-                                   const llvm::StringSet<> &Suppress) {
+                                   const llvm::StringSet<> &Suppress,
+                                   const LangOptions &LangOpts) {
+  // Don't complain about header-only stuff in mainfiles if it's a header.
+  // FIXME: would be cleaner to suppress in clang, once we decide whether the
+  //        behavior should be to silently-ignore or respect the pragma.
+  if (ID == diag::pp_pragma_sysheader_in_main_file && LangOpts.IsHeaderFile)
+    return true;
+
   if (const char *CodePtr = getDiagnosticCode(ID)) {
     if (Suppress.contains(normalizeSuppressedCode(CodePtr)))
       return true;
diff --git a/clang-tools-extra/clangd/ParsedAST.cpp b/clang-tools-extra/clangd/ParsedAST.cpp
--- a/clang-tools-extra/clangd/ParsedAST.cpp
+++ b/clang-tools-extra/clangd/ParsedAST.cpp
@@ -445,7 +445,8 @@
     ASTDiags.setLevelAdjuster([&](DiagnosticsEngine::Level DiagLevel,
                                   const clang::Diagnostic &Info) {
       if (Cfg.Diagnostics.SuppressAll ||
-          isBuiltinDiagnosticSuppressed(Info.getID(), Cfg.Diagnostics.Suppress))
+          isBuiltinDiagnosticSuppressed(Info.getID(), Cfg.Diagnostics.Suppress,
+                                        Clang->getLangOpts()))
         return DiagnosticsEngine::Ignored;
 
       auto It = OverriddenSeverity.find(Info.getID());
diff --git a/clang-tools-extra/clangd/Preamble.cpp b/clang-tools-extra/clangd/Preamble.cpp
--- a/clang-tools-extra/clangd/Preamble.cpp
+++ b/clang-tools-extra/clangd/Preamble.cpp
@@ -350,7 +350,8 @@
   PreambleDiagnostics.setLevelAdjuster([&](DiagnosticsEngine::Level DiagLevel,
                                            const clang::Diagnostic &Info) {
     if (Cfg.Diagnostics.SuppressAll ||
-        isBuiltinDiagnosticSuppressed(Info.getID(), Cfg.Diagnostics.Suppress))
+        isBuiltinDiagnosticSuppressed(Info.getID(), Cfg.Diagnostics.Suppress,
+                                      *CI.getLangOpts()))
       return DiagnosticsEngine::Ignored;
     switch (Info.getID()) {
     case diag::warn_no_newline_eof:
diff --git a/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp b/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
--- a/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
+++ b/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
@@ -277,19 +277,20 @@
                                    "unreachable-code", "unused-variable",
                                    "typecheck_bool_condition",
                                    "unexpected_friend", "warn_alloca"));
-  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(diag::warn_unreachable,
-                                            Conf.Diagnostics.Suppress));
+  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(
+      diag::warn_unreachable, Conf.Diagnostics.Suppress, LangOptions()));
   // Subcategory not respected/suppressed.
-  EXPECT_FALSE(isBuiltinDiagnosticSuppressed(diag::warn_unreachable_break,
-                                             Conf.Diagnostics.Suppress));
-  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(diag::warn_unused_variable,
-                                            Conf.Diagnostics.Suppress));
+  EXPECT_FALSE(isBuiltinDiagnosticSuppressed(
+      diag::warn_unreachable_break, Conf.Diagnostics.Suppress, LangOptions()));
+  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(
+      diag::warn_unused_variable, Conf.Diagnostics.Suppress, LangOptions()));
   EXPECT_TRUE(isBuiltinDiagnosticSuppressed(diag::err_typecheck_bool_condition,
-                                            Conf.Diagnostics.Suppress));
-  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(diag::err_unexpected_friend,
-                                            Conf.Diagnostics.Suppress));
-  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(diag::warn_alloca,
-                                            Conf.Diagnostics.Suppress));
+                                            Conf.Diagnostics.Suppress,
+                                            LangOptions()));
+  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(
+      diag::err_unexpected_friend, Conf.Diagnostics.Suppress, LangOptions()));
+  EXPECT_TRUE(isBuiltinDiagnosticSuppressed(
+      diag::warn_alloca, Conf.Diagnostics.Suppress, LangOptions()));
 
   Frag.Diagnostics.Suppress.emplace_back("*");
   EXPECT_TRUE(compileAndApply());
diff --git a/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp b/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
--- a/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
+++ b/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
@@ -771,6 +771,17 @@
                                 Not(WithFix(_)))));
 }
 
+TEST(DiagnosticsTest, PragmaSystemHeader) {
+  Annotations Test("#pragma clang [[system_header]]\n");
+  auto TU = TestTU::withCode(Test.code());
+  EXPECT_THAT(
+      *TU.build().getDiagnostics(),
+      ElementsAre(AllOf(
+          Diag(Test.range(), "#pragma system_header ignored in main file"))));
+  TU.Filename = "TestTU.h";
+  EXPECT_THAT(*TU.build().getDiagnostics(), IsEmpty());
+}
+
 TEST(ClangdTest, MSAsm) {
   // Parsing MS assembly tries to use the target MCAsmInfo, which we don't link.
   // We used to crash here. Now clang emits a diagnostic, which we filter out.