diff --git a/clang/docs/ReleaseNotes.rst b/clang/docs/ReleaseNotes.rst
index 08ffb08e341ab..79534687139cc 100644
--- a/clang/docs/ReleaseNotes.rst
+++ b/clang/docs/ReleaseNotes.rst
@@ -444,6 +444,8 @@ Improvements to Clang's diagnostics
 - ``-Wzero-as-null-pointer-constant`` diagnostic is no longer emitted when using ``__null``
   (or, more commonly, ``NULL`` when the platform defines it as ``__null``) to be more consistent
   with GCC.
+- Clang will warn on deprecated specializations used in system headers when their instantiation
+  is caused by user code.
 
 Improvements to Clang's time-trace
 ----------------------------------
diff --git a/clang/include/clang/Sema/Sema.h b/clang/include/clang/Sema/Sema.h
index 501dc01200a1c..73981a4d657d4 100644
--- a/clang/include/clang/Sema/Sema.h
+++ b/clang/include/clang/Sema/Sema.h
@@ -8464,6 +8464,8 @@ class Sema final {
       ArrayRef<TemplateArgument> SugaredConverted,
       ArrayRef<TemplateArgument> CanonicalConverted, bool &HasDefaultArg);
 
+  SourceLocation getTopMostPointOfInstantiation(const NamedDecl *) const;
+
   /// Specifies the context in which a particular template
   /// argument is being checked.
   enum CheckTemplateArgumentKind {
diff --git a/clang/lib/Sema/SemaAvailability.cpp b/clang/lib/Sema/SemaAvailability.cpp
index 84c06566387cc..846a31a796730 100644
--- a/clang/lib/Sema/SemaAvailability.cpp
+++ b/clang/lib/Sema/SemaAvailability.cpp
@@ -536,6 +536,29 @@ static void DoEmitAvailabilityWarning(Sema &S, AvailabilityResult K,
     }
   }
 
+  // We emit deprecation warning for deprecated specializations
+  // when their instantiation stacks originate outside
+  // of a system header, even if the diagnostics is suppresed at the
+  // point of definition.
+  SourceLocation InstantiationLoc =
+      S.getTopMostPointOfInstantiation(ReferringDecl);
+  bool ShouldAllowWarningInSystemHeader =
+      InstantiationLoc != Loc &&
+      !S.getSourceManager().isInSystemHeader(InstantiationLoc);
+  struct AllowWarningInSystemHeaders {
+    AllowWarningInSystemHeaders(DiagnosticsEngine &E,
+                                bool AllowWarningInSystemHeaders)
+        : Engine(E), Prev(E.getSuppressSystemWarnings()) {
+      E.setSuppressSystemWarnings(!AllowWarningInSystemHeaders);
+    }
+    ~AllowWarningInSystemHeaders() { Engine.setSuppressSystemWarnings(Prev); }
+
+  private:
+    DiagnosticsEngine &Engine;
+    bool Prev;
+  } SystemWarningOverrideRAII(S.getDiagnostics(),
+                              ShouldAllowWarningInSystemHeader);
+
   if (!Message.empty()) {
     S.Diag(Loc, diag_message) << ReferringDecl << Message << FixIts;
     if (ObjCProperty)
diff --git a/clang/lib/Sema/SemaTemplate.cpp b/clang/lib/Sema/SemaTemplate.cpp
index 766ebd90fded0..c188dd34014a4 100644
--- a/clang/lib/Sema/SemaTemplate.cpp
+++ b/clang/lib/Sema/SemaTemplate.cpp
@@ -11601,3 +11601,25 @@ void Sema::checkSpecializationReachability(SourceLocation Loc,
                                           Sema::AcceptableKind::Reachable)
       .check(Spec);
 }
+
+/// Returns the top most location responsible for the definition of \p N.
+/// If \p N is a a template specialization, this is the location
+/// of the top of the instantiation stack.
+/// Otherwise, the location of \p N is returned.
+SourceLocation Sema::getTopMostPointOfInstantiation(const NamedDecl *N) const {
+  if (!getLangOpts().CPlusPlus || CodeSynthesisContexts.empty())
+    return N->getLocation();
+  if (const auto *FD = dyn_cast<FunctionDecl>(N)) {
+    if (!FD->isFunctionTemplateSpecialization())
+      return FD->getLocation();
+  } else if (!isa<ClassTemplateSpecializationDecl,
+                  VarTemplateSpecializationDecl>(N)) {
+    return N->getLocation();
+  }
+  for (const CodeSynthesisContext &CSC : CodeSynthesisContexts) {
+    if (!CSC.isInstantiationRecord() || CSC.PointOfInstantiation.isInvalid())
+      continue;
+    return CSC.PointOfInstantiation;
+  }
+  return N->getLocation();
+}
diff --git a/clang/test/SemaCXX/warn-deprecated-specializations-in-system-headers.cpp b/clang/test/SemaCXX/warn-deprecated-specializations-in-system-headers.cpp
new file mode 100644
index 0000000000000..79c9d339b6f20
--- /dev/null
+++ b/clang/test/SemaCXX/warn-deprecated-specializations-in-system-headers.cpp
@@ -0,0 +1,28 @@
+// RUN: %clang_cc1 -fsyntax-only -verify %s
+
+#ifdef BE_THE_HEADER
+#pragma clang system_header
+
+template <typename T>
+struct traits;
+
+template <>
+struct [[deprecated]] traits<int> {}; // expected-note {{'traits<int>' has been explicitly marked deprecated here}}
+
+template<typename T, typename Trait = traits<T>>  // expected-warning {{'traits<int>' is deprecated}}
+struct basic_string {};
+
+// should not warn, defined and used in system headers
+using __do_what_i_say_not_what_i_do  = traits<int> ;
+
+template<typename T, typename Trait = traits<double>>
+struct should_not_warn {};
+
+#else
+#define BE_THE_HEADER
+#include __FILE__
+
+basic_string<int> test1; // expected-note {{in instantiation of default argument for 'basic_string<int>' required here}}
+should_not_warn<int> test2;
+
+#endif