diff --git a/clang/include/clang/Tooling/Inclusions/HeaderIncludes.h b/clang/include/clang/Tooling/Inclusions/HeaderIncludes.h
--- a/clang/include/clang/Tooling/Inclusions/HeaderIncludes.h
+++ b/clang/include/clang/Tooling/Inclusions/HeaderIncludes.h
@@ -40,8 +40,6 @@
   const IncludeStyle Style;
   bool IsMainFile;
   std::string FileName;
-  // This refers to a substring in FileName.
-  StringRef FileStem;
   SmallVector<llvm::Regex, 4> CategoryRegexs;
 };
 
diff --git a/clang/lib/Tooling/Inclusions/HeaderIncludes.cpp b/clang/lib/Tooling/Inclusions/HeaderIncludes.cpp
--- a/clang/lib/Tooling/Inclusions/HeaderIncludes.cpp
+++ b/clang/lib/Tooling/Inclusions/HeaderIncludes.cpp
@@ -190,7 +190,6 @@
 IncludeCategoryManager::IncludeCategoryManager(const IncludeStyle &Style,
                                                StringRef FileName)
     : Style(Style), FileName(FileName) {
-  FileStem = matchingStem(FileName);
   for (const auto &Category : Style.IncludeCategories)
     CategoryRegexs.emplace_back(Category.Regex, llvm::Regex::IgnoreCase);
   IsMainFile = FileName.endswith(".c") || FileName.endswith(".cc") ||
@@ -234,16 +233,30 @@
   if (!IncludeName.startswith("\""))
     return false;
 
+  IncludeName =
+      IncludeName.drop_front(1).drop_back(1); // remove the surrounding "" or <>
   // Not matchingStem: implementation files may have compound extensions but
   // headers may not.
-  StringRef HeaderStem =
-      llvm::sys::path::stem(IncludeName.drop_front(1).drop_back(
-          1) /* remove the surrounding "" or <> */);
-  if (FileStem.startswith(HeaderStem) ||
-      FileStem.startswith_lower(HeaderStem)) {
+  StringRef HeaderStem = llvm::sys::path::stem(IncludeName);
+  StringRef FileStem = llvm::sys::path::stem(FileName); // foo.cu for foo.cu.cc
+  StringRef MatchingFileStem = matchingStem(FileName);  // foo for foo.cu.cc
+  // main-header examples:
+  //   1) foo.h => foo.cc
+  //   2) foo.h => foo.<name>.cc (e.g. foo.cu.cc)
+  //   3) foo.<name>.h => foo.<name>.cc
+  //
+  // non-main-header examples:
+  //  foo.proto.h => foo.cc
+  //  foo.h => bar.cc
+  StringRef Matching;
+  if (MatchingFileStem.startswith_lower(HeaderStem))
+    Matching = MatchingFileStem; // example 1), 2)
+  else if (FileStem.equals_lower(HeaderStem))
+    Matching = FileStem; // example 3)
+  if (!Matching.empty()) {
     llvm::Regex MainIncludeRegex(HeaderStem.str() + Style.IncludeIsMainRegex,
                                  llvm::Regex::IgnoreCase);
-    if (MainIncludeRegex.match(FileStem))
+    if (MainIncludeRegex.match(Matching))
       return true;
   }
   return false;
diff --git a/clang/unittests/Format/SortIncludesTest.cpp b/clang/unittests/Format/SortIncludesTest.cpp
--- a/clang/unittests/Format/SortIncludesTest.cpp
+++ b/clang/unittests/Format/SortIncludesTest.cpp
@@ -151,7 +151,7 @@
   EXPECT_TRUE(sortIncludes(FmtStyle, Code, GetCodeRange(Code), "a.cc").empty());
 }
 
-TEST_F(SortIncludesTest, NoMainFileHeader) {
+TEST_F(SortIncludesTest, MainFileHeader) {
   std::string Code = "#include <string>\n"
                      "\n"
                      "#include \"a/extra_action.proto.h\"\n";
@@ -159,6 +159,13 @@
   EXPECT_TRUE(
       sortIncludes(FmtStyle, Code, GetCodeRange(Code), "a/extra_action.cc")
           .empty());
+
+  EXPECT_EQ("#include \"foo.bar.h\"\n"
+            "\n"
+            "#include \"a.h\"\n",
+            sort("#include \"a.h\"\n"
+                 "#include \"foo.bar.h\"\n",
+                 "foo.bar.cc"));
 }
 
 TEST_F(SortIncludesTest, SortedIncludesInMultipleBlocksAreMerged) {