diff --git a/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.h b/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.h
--- a/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.h
+++ b/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.h
@@ -49,6 +49,7 @@
   bool isLanguageVersionSupported(const LangOptions &LangOpts) const override {
     return LangOpts.CPlusPlus;
   }
+  void storeOptions(ClangTidyOptions::OptionMap &Opts) override;
   void registerPPCallbacks(const SourceManager &SM, Preprocessor *PP,
                            Preprocessor *ModuleExpanderPP) override;
   void registerMatchers(ast_matchers::MatchFinder *Finder) override;
@@ -59,6 +60,7 @@
   friend class detail::IncludeModernizePPCallbacks;
   friend class detail::ExternCRefutationVisitor;
   std::vector<detail::IncludeMarker> IncludesToBeProcessed;
+  bool WarnIntoHeaders;
 };
 
 } // namespace modernize
diff --git a/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.cpp b/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.cpp
--- a/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.cpp
+++ b/clang-tools-extra/clang-tidy/modernize/DeprecatedHeadersCheck.cpp
@@ -24,7 +24,8 @@
 class IncludeModernizePPCallbacks : public PPCallbacks {
 public:
   explicit IncludeModernizePPCallbacks(DeprecatedHeadersCheck &Check,
-                                       LangOptions LangOpts);
+                                       LangOptions LangOpts,
+                                       const SourceManager &SM);
 
   void InclusionDirective(SourceLocation HashLoc, const Token &IncludeTok,
                           StringRef FileName, bool IsAngled,
@@ -38,6 +39,7 @@
   LangOptions LangOpts;
   llvm::StringMap<std::string> CStyledHeaderToCxx;
   llvm::StringSet<> DeleteHeaders;
+  const SourceManager &SM;
 };
 
 class ExternCRefutationVisitor
@@ -72,12 +74,17 @@
 
 DeprecatedHeadersCheck::DeprecatedHeadersCheck(StringRef Name,
                                                ClangTidyContext *Context)
-    : ClangTidyCheck(Name, Context) {}
+    : ClangTidyCheck(Name, Context),
+      WarnIntoHeaders(Options.get("WarnIntoHeaders", false)) {}
+
+void DeprecatedHeadersCheck::storeOptions(ClangTidyOptions::OptionMap &Opts) {
+  Options.store(Opts, "WarnIntoHeaders", WarnIntoHeaders);
+}
 
 void DeprecatedHeadersCheck::registerPPCallbacks(
     const SourceManager &SM, Preprocessor *PP, Preprocessor *ModuleExpanderPP) {
   PP->addPPCallbacks(::std::make_unique<detail::IncludeModernizePPCallbacks>(
-      *this, getLangOpts()));
+      *this, getLangOpts(), PP->getSourceManager()));
 }
 void DeprecatedHeadersCheck::registerMatchers(
     ast_matchers::MatchFinder *Finder) {
@@ -121,8 +128,9 @@
 }
 
 detail::IncludeModernizePPCallbacks::IncludeModernizePPCallbacks(
-    DeprecatedHeadersCheck &Check, LangOptions LangOpts)
-    : Check(Check), LangOpts(LangOpts) {
+    DeprecatedHeadersCheck &Check, LangOptions LangOpts,
+    const SourceManager &SM)
+    : Check(Check), LangOpts(LangOpts), SM(SM) {
   for (const auto &KeyValue :
        std::vector<std::pair<llvm::StringRef, std::string>>(
            {{"assert.h", "cassert"},
@@ -168,6 +176,12 @@
     bool IsAngled, CharSourceRange FilenameRange, Optional<FileEntryRef> File,
     StringRef SearchPath, StringRef RelativePath, const Module *Imported,
     SrcMgr::CharacteristicKind FileType) {
+
+  // If we don't want to warn for non-main file reports and this is one, skip
+  // it.
+  if (!Check.WarnIntoHeaders && !SM.isInMainFile(HashLoc))
+    return;
+
   // FIXME: Take care of library symbols from the global namespace.
   //
   // Reasonable options for the check:
diff --git a/clang-tools-extra/docs/ReleaseNotes.rst b/clang-tools-extra/docs/ReleaseNotes.rst
--- a/clang-tools-extra/docs/ReleaseNotes.rst
+++ b/clang-tools-extra/docs/ReleaseNotes.rst
@@ -174,6 +174,10 @@
   <clang-tidy/checks/modernize-deprecated-headers>` involving including
   C header files from C++ files wrapped by ``extern "C" { ... }`` blocks.
   Such includes will be ignored by now.
+  By default now it doesn't warn for including deprecated headers from header
+  files, since that header file might be used from C source files. By passing
+  the ``WarnIntoHeaders=true`` option if header files of the project only
+  included by c++ source files.
 
 - Improved :doc:`performance-inefficient-vector-operation
   <clang-tidy/checks/performance-inefficient-vector-operation>` to work when
diff --git a/clang-tools-extra/test/clang-tidy/checkers/modernize-deprecated-headers-extern-c.cpp b/clang-tools-extra/test/clang-tidy/checkers/modernize-deprecated-headers-extern-c.cpp
--- a/clang-tools-extra/test/clang-tidy/checkers/modernize-deprecated-headers-extern-c.cpp
+++ b/clang-tools-extra/test/clang-tidy/checkers/modernize-deprecated-headers-extern-c.cpp
@@ -8,6 +8,13 @@
 // RUN:   && cp %S/Inputs/modernize-deprecated-headers/mylib.h       %t/usr/mylib.h
 
 // RUN: %check_clang_tidy -std=c++11 %s modernize-deprecated-headers %t \
+// RUN:   -check-suffixes=DEFAULT \
+// RUN:   --header-filter='.*' --system-headers \
+// RUN:   -- -I %t/usr -isystem %t/sys -isystem %S/Inputs/modernize-deprecated-headers
+
+// RUN: %check_clang_tidy -std=c++11 %s modernize-deprecated-headers %t \
+// RUN:   -check-suffixes=DEFAULT,WARN-INTO-HEADERS \
+// RUN:   -config="{CheckOptions: [{key: modernize-deprecated-headers.WarnIntoHeaders, value: 'true'}]}" \
 // RUN:   --header-filter='.*' --system-headers \
 // RUN:   -- -I %t/usr -isystem %t/sys -isystem %S/Inputs/modernize-deprecated-headers
 
@@ -18,20 +25,20 @@
 extern "C++" {
 // We should still have the warnings here.
 #include <stdbool.h>
-// CHECK-MESSAGES: :[[@LINE-1]]:10: warning: including 'stdbool.h' has no effect in C++; consider removing it [modernize-deprecated-headers]
+// CHECK-MESSAGES-DEFAULT: :[[@LINE-1]]:10: warning: including 'stdbool.h' has no effect in C++; consider removing it [modernize-deprecated-headers]
 }
 
 #include <assert.h>
-// CHECK-MESSAGES: :[[@LINE-1]]:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
+// CHECK-MESSAGES-DEFAULT: :[[@LINE-1]]:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
 
 #include <stdbool.h>
-// CHECK-MESSAGES: :[[@LINE-1]]:10: warning: including 'stdbool.h' has no effect in C++; consider removing it [modernize-deprecated-headers]
+// CHECK-MESSAGES-DEFAULT: :[[@LINE-1]]:10: warning: including 'stdbool.h' has no effect in C++; consider removing it [modernize-deprecated-headers]
 
 #include <mysystemlib.h> // FIXME: We should have no warning into system headers.
-// CHECK-MESSAGES: mysystemlib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
+// CHECK-MESSAGES-WARN-INTO-HEADERS: mysystemlib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
 
 #include <mylib.h>
-// CHECK-MESSAGES: mylib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
+// CHECK-MESSAGES-WARN-INTO-HEADERS: mylib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
 
 namespace wrapping {
 extern "C" {