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
@@ -188,6 +188,10 @@
   if (!CheckHeaderFile && !SM.isInMainFile(HashLoc))
     return;
 
+  // Ignore system headers.
+  if (SM.isInSystemHeader(HashLoc))
+    return;
+
   // FIXME: Take care of library symbols from the global namespace.
   //
   // Reasonable options for the check:
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
@@ -34,8 +34,7 @@
 #include <stdbool.h>
 // 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-CHECK-HEADER-FILE: mysystemlib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]
+#include <mysystemlib.h> // no-warning: Don't warn into system headers.
 
 #include <mylib.h>
 // CHECK-MESSAGES-CHECK-HEADER-FILE: mylib.h:1:10: warning: inclusion of deprecated C++ header 'assert.h'; consider using 'cassert' instead [modernize-deprecated-headers]