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 +879,13 @@
 }
 
 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 the main file is a
+  // header. (Not clear if this is reasonable to suppress in clang).
+  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: