diff --git a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningTool.h b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningTool.h
--- a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningTool.h
+++ b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningTool.h
@@ -68,7 +68,9 @@
 class DependencyScanningTool {
 public:
   /// Construct a dependency scanning tool.
-  DependencyScanningTool(DependencyScanningService &Service);
+  DependencyScanningTool(DependencyScanningService &Service,
+                         llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS =
+                             llvm::vfs::createPhysicalFileSystem());
 
   /// Print out the dependency information into a string using the dependency
   /// file format that is specified in the options (-MD is the default) and
diff --git a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningWorker.h b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningWorker.h
--- a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningWorker.h
+++ b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningWorker.h
@@ -52,7 +52,8 @@
 /// using the regular processing run.
 class DependencyScanningWorker {
 public:
-  DependencyScanningWorker(DependencyScanningService &Service);
+  DependencyScanningWorker(DependencyScanningService &Service,
+                           llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS);
 
   /// Run the dependency scanning tool for a given clang driver command-line,
   /// and report the discovered dependencies to the provided consumer. If \p
diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
@@ -50,8 +50,9 @@
 }
 
 DependencyScanningTool::DependencyScanningTool(
-    DependencyScanningService &Service)
-    : Worker(Service) {}
+    DependencyScanningService &Service,
+    llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS)
+    : Worker(Service, std::move(FS)) {}
 
 llvm::Expected<std::string> DependencyScanningTool::getDependencyFile(
     const std::vector<std::string> &CommandLine, StringRef CWD,
diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -264,7 +264,8 @@
 } // end anonymous namespace
 
 DependencyScanningWorker::DependencyScanningWorker(
-    DependencyScanningService &Service)
+    DependencyScanningService &Service,
+    llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS)
     : Format(Service.getFormat()), OptimizeArgs(Service.canOptimizeArgs()) {
   PCHContainerOps = std::make_shared<PCHContainerOperations>();
   PCHContainerOps->registerReader(
@@ -274,8 +275,8 @@
   PCHContainerOps->registerWriter(
       std::make_unique<ObjectFilePCHContainerWriter>());
 
-  auto OverlayFS = llvm::makeIntrusiveRefCnt<llvm::vfs::OverlayFileSystem>(
-      llvm::vfs::createPhysicalFileSystem());
+  auto OverlayFS =
+      llvm::makeIntrusiveRefCnt<llvm::vfs::OverlayFileSystem>(std::move(FS));
   InMemoryFS = llvm::makeIntrusiveRefCnt<llvm::vfs::InMemoryFileSystem>();
   OverlayFS->pushOverlay(InMemoryFS);
   RealFS = OverlayFS;
diff --git a/clang/unittests/Tooling/DependencyScannerTest.cpp b/clang/unittests/Tooling/DependencyScannerTest.cpp
--- a/clang/unittests/Tooling/DependencyScannerTest.cpp
+++ b/clang/unittests/Tooling/DependencyScannerTest.cpp
@@ -14,19 +14,21 @@
 #include "clang/Frontend/FrontendAction.h"
 #include "clang/Frontend/FrontendActions.h"
 #include "clang/Tooling/CompilationDatabase.h"
-#include "clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h"
+#include "clang/Tooling/DependencyScanning/DependencyScanningTool.h"
 #include "clang/Tooling/Tooling.h"
 #include "llvm/ADT/STLExtras.h"
 #include "llvm/MC/TargetRegistry.h"
 #include "llvm/Support/FormatVariadic.h"
 #include "llvm/Support/Path.h"
 #include "llvm/Support/TargetSelect.h"
+#include "llvm/Testing/Support/Error.h"
 #include "gtest/gtest.h"
 #include <algorithm>
 #include <string>
 
 using namespace clang;
 using namespace tooling;
+using namespace dependencies;
 
 namespace {
 
@@ -203,3 +205,33 @@
   EXPECT_EQ(convert_to_slash(Deps[4]), "/root/header.h");
   EXPECT_EQ(convert_to_slash(Deps[5]), "/root/symlink.h");
 }
+
+TEST(DependencyScanner, ScanDepsWithFS) {
+  std::vector<std::string> CommandLine = {"clang", "-c", "test.cpp",
+                                          "-o"
+                                          "test.cpp.o"};
+  StringRef CWD = "/root";
+
+  auto VFS = new llvm::vfs::InMemoryFileSystem();
+  VFS->setCurrentWorkingDirectory(CWD);
+  auto Sept = llvm::sys::path::get_separator();
+  std::string HeaderPath =
+      std::string(llvm::formatv("{0}root{0}header.h", Sept));
+  std::string TestPath = std::string(llvm::formatv("{0}root{0}test.cpp", Sept));
+
+  VFS->addFile(HeaderPath, 0, llvm::MemoryBuffer::getMemBuffer("\n"));
+  VFS->addFile(TestPath, 0,
+               llvm::MemoryBuffer::getMemBuffer("#include \"header.h\"\n"));
+
+  DependencyScanningService Service(ScanningMode::DependencyDirectivesScan,
+                                    ScanningOutputFormat::Make);
+  DependencyScanningTool ScanTool(Service, VFS);
+
+  std::string DepFile;
+  ASSERT_THAT_ERROR(
+      ScanTool.getDependencyFile(CommandLine, CWD).moveInto(DepFile),
+      llvm::Succeeded());
+  using llvm::sys::path::convert_to_slash;
+  EXPECT_EQ(convert_to_slash(DepFile),
+            "test.cpp.o: /root/test.cpp /root/header.h\n");
+}