diff --git a/clang/lib/Tooling/JSONCompilationDatabase.cpp b/clang/lib/Tooling/JSONCompilationDatabase.cpp
--- a/clang/lib/Tooling/JSONCompilationDatabase.cpp
+++ b/clang/lib/Tooling/JSONCompilationDatabase.cpp
@@ -419,14 +419,13 @@
     SmallString<128> NativeFilePath;
     if (llvm::sys::path::is_relative(FileName)) {
       SmallString<8> DirectoryStorage;
-      SmallString<128> AbsolutePath(
-          Directory->getValue(DirectoryStorage));
+      SmallString<128> AbsolutePath(Directory->getValue(DirectoryStorage));
       llvm::sys::path::append(AbsolutePath, FileName);
-      llvm::sys::path::remove_dots(AbsolutePath, /*remove_dot_dot=*/ true);
       llvm::sys::path::native(AbsolutePath, NativeFilePath);
     } else {
       llvm::sys::path::native(FileName, NativeFilePath);
     }
+    llvm::sys::path::remove_dots(NativeFilePath, /*remove_dot_dot=*/true);
     auto Cmd = CompileCommandRef(Directory, File, *Command, Output);
     IndexByFile[NativeFilePath].push_back(Cmd);
     AllCommands.push_back(Cmd);
diff --git a/clang/unittests/Tooling/CompilationDatabaseTest.cpp b/clang/unittests/Tooling/CompilationDatabaseTest.cpp
--- a/clang/unittests/Tooling/CompilationDatabaseTest.cpp
+++ b/clang/unittests/Tooling/CompilationDatabaseTest.cpp
@@ -92,16 +92,32 @@
   expected_files.push_back(std::string(PathStorage.str()));
   llvm::sys::path::native("//net/file1", PathStorage);
   expected_files.push_back(std::string(PathStorage.str()));
+  llvm::sys::path::native("//net/dir/file3", PathStorage);
+  expected_files.push_back(std::string(PathStorage.str()));
   EXPECT_EQ(expected_files,
-            getAllFiles("[{\"directory\":\"//net/dir\","
-                        "\"command\":\"command\","
-                        "\"file\":\"file1\"},"
-                        " {\"directory\":\"//net/dir\","
-                        "\"command\":\"command\","
-                        "\"file\":\"../file1\"},"
-                        " {\"directory\":\"//net/dir\","
-                        "\"command\":\"command\","
-                        "\"file\":\"file2\"}]",
+            getAllFiles(R"json(
+            [
+              {
+                "directory": "//net/dir",
+                "command": "command",
+                "file": "file1"
+              },
+              {
+                "directory": "//net/dir",
+                "command": "command",
+                "file": "../file1"
+              },
+              {
+                "directory": "//net/dir",
+                "command": "command",
+                "file": "file2"
+              },
+              {
+                "directory": "//net/dir",
+                "command": "command",
+                "file": "//net/dir/foo/../file3"
+              }
+            ])json",
                         ErrorMessage, JSONCommandLineSyntax::Gnu))
       << ErrorMessage;
 }