diff --git a/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.h b/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.h
--- a/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.h
+++ b/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.h
@@ -10,6 +10,7 @@
 #define LLVM_CLANG_TOOLS_EXTRA_CLANG_TIDY_MODERNIZE_CONCATNESTEDNAMESPACESCHECK_H
 
 #include "../ClangTidyCheck.h"
+#include "../utils/HeaderFileExtensionsUtils.h"
 #include "llvm/ADT/SmallString.h"
 #include "llvm/ADT/SmallVector.h"
 
@@ -17,10 +18,16 @@
 namespace tidy {
 namespace modernize {
 
+/// The check supports these options:
+///   - `HeaderFileExtensions`: a comma-separated list of filename extensions of
+///     header files (The filename extensions should not contain "." prefix).
+///     "h,hh,hpp,hxx" by default.
+///     For extension-less header files, using an empty string or leaving an
+///     empty string between "," if there are other filename extensions.
 class ConcatNestedNamespacesCheck : public ClangTidyCheck {
 public:
-  ConcatNestedNamespacesCheck(StringRef Name, ClangTidyContext *Context)
-      : ClangTidyCheck(Name, Context) {}
+  ConcatNestedNamespacesCheck(StringRef Name, ClangTidyContext *Context);
+  void storeOptions(ClangTidyOptions::OptionMap &Opts) override;
   void registerMatchers(ast_matchers::MatchFinder *Finder) override;
   void check(const ast_matchers::MatchFinder::MatchResult &Result) override;
 
@@ -32,6 +39,8 @@
                         const SourceRange &BackReplacement);
   NamespaceString concatNamespaces();
   NamespaceContextVec Namespaces;
+  const std::string RawStringHeaderFileExtensions;
+  utils::HeaderFileExtensionsSet HeaderFileExtensions;
 };
 } // namespace modernize
 } // namespace tidy
diff --git a/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.cpp b/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.cpp
--- a/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.cpp
+++ b/clang-tools-extra/clang-tidy/modernize/ConcatNestedNamespacesCheck.cpp
@@ -61,6 +61,22 @@
   return Result;
 }
 
+ConcatNestedNamespacesCheck::ConcatNestedNamespacesCheck(
+    StringRef Name, ClangTidyContext *Context)
+    : ClangTidyCheck(Name, Context),
+      RawStringHeaderFileExtensions(Options.getLocalOrGlobal(
+          "HeaderFileExtensions", utils::defaultHeaderFileExtensions())) {
+  if (!utils::parseHeaderFileExtensions(RawStringHeaderFileExtensions,
+                                        HeaderFileExtensions, ','))
+    llvm::errs() << "Invalid header file extension: "
+                 << RawStringHeaderFileExtensions << "\n";
+}
+
+void ConcatNestedNamespacesCheck::storeOptions(
+    ClangTidyOptions::OptionMap &Opts) {
+  Options.store(Opts, "HeaderFileExtensions", RawStringHeaderFileExtensions);
+}
+
 void ConcatNestedNamespacesCheck::registerMatchers(
     ast_matchers::MatchFinder *Finder) {
   if (!getLangOpts().CPlusPlus17)
@@ -85,7 +101,9 @@
   if (!locationsInSameFile(Sources, ND.getBeginLoc(), ND.getRBraceLoc()))
     return;
 
-  if (!Sources.isInMainFile(ND.getBeginLoc()))
+  if (!Sources.isInMainFile(ND.getBeginLoc()) &&
+      !utils::isSpellingLocInHeaderFile(ND.getBeginLoc(), *Result.SourceManager,
+                                        HeaderFileExtensions))
     return;
 
   if (anonymousOrInlineNamespace(ND))
diff --git a/clang-tools-extra/docs/clang-tidy/checks/modernize-concat-nested-namespaces.rst b/clang-tools-extra/docs/clang-tidy/checks/modernize-concat-nested-namespaces.rst
--- a/clang-tools-extra/docs/clang-tidy/checks/modernize-concat-nested-namespaces.rst
+++ b/clang-tools-extra/docs/clang-tidy/checks/modernize-concat-nested-namespaces.rst
@@ -47,3 +47,13 @@
   }
   }
 
+Options
+-------
+
+.. option:: HeaderFileExtensions
+
+   A comma-separated list of filename extensions of header files (the filename
+   extensions should not contain "." prefix). Default is "h,hh,hpp,hxx".
+   For header files without an extension, use an empty string (if there are no
+   other desired extensions) or leave an empty element in the list. e.g.,
+   "h,hh,hpp,hxx," (note the trailing comma).
diff --git a/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.h b/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.h
new file mode 100644
--- /dev/null
+++ b/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.h
@@ -0,0 +1,9 @@
+#pragma once
+
+namespace foo {
+namespace bar {
+namespace baz {
+struct S {};
+} // namespace baz
+} // namespace bar
+} // namespace foo
diff --git a/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.cpp b/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.cpp
--- a/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.cpp
+++ b/clang-tools-extra/test/clang-tidy/modernize-concat-nested-namespaces.cpp
@@ -1,4 +1,7 @@
-// RUN: %check_clang_tidy %s modernize-concat-nested-namespaces %t -- -- -std=c++17
+// RUN: cp %S/modernize-concat-nested-namespaces.h %T/modernize-concat-nested-namespaces.h
+// RUN: %check_clang_tidy %s modernize-concat-nested-namespaces %t -- -header-filter="concat" -- -std=c++17 -I %T
+
+#include "modernize-concat-nested-namespaces.h"
 
 namespace n1 {}
 
@@ -159,3 +162,7 @@
 
   return 0;
 }
+
+// Checks for header file:
+
+// CHECK-MESSAGES: modernize-concat-nested-namespaces.h:{{.*}} warning: nested namespaces can be concatenated [modernize-concat-nested-namespaces]