Index: clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
===================================================================
--- clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -44,28 +44,6 @@
   DependencyConsumer &C;
 };
 
-/// A proxy file system that doesn't call `chdir` when changing the working
-/// directory of a clang tool.
-class ProxyFileSystemWithoutChdir : public llvm::vfs::ProxyFileSystem {
-public:
-  ProxyFileSystemWithoutChdir(
-      llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS)
-      : ProxyFileSystem(std::move(FS)) {}
-
-  llvm::ErrorOr<std::string> getCurrentWorkingDirectory() const override {
-    assert(!CWD.empty() && "empty CWD");
-    return CWD;
-  }
-
-  std::error_code setCurrentWorkingDirectory(const Twine &Path) override {
-    CWD = Path.str();
-    return {};
-  }
-
-private:
-  std::string CWD;
-};
-
 /// A clang tool that runs the preprocessor in a mode that's optimized for
 /// dependency scanning for the given compiler invocation.
 class DependencyScanningAction : public tooling::ToolAction {
@@ -176,7 +154,10 @@
     : Format(Service.getFormat()) {
   DiagOpts = new DiagnosticOptions();
   PCHContainerOps = std::make_shared<PCHContainerOperations>();
-  RealFS = new ProxyFileSystemWithoutChdir(llvm::vfs::getRealFileSystem());
+
+  llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> PhysicalFileSystem(
+      llvm::vfs::createPhysicalFileSystem().release());
+  RealFS = new llvm::vfs::ProxyFileSystem(PhysicalFileSystem);
   if (Service.canSkipExcludedPPRanges())
     PPSkipMappings =
         std::make_unique<ExcludedPreprocessorDirectiveSkipMapping>();
Index: clang/test/ClangScanDeps/Inputs/relative_directory.json
===================================================================
--- /dev/null
+++ clang/test/ClangScanDeps/Inputs/relative_directory.json
@@ -0,0 +1,12 @@
+[
+{
+  "directory": "DIR",
+  "command": "clang -E Inputs/relative_directory_input1.cpp -IInputs",
+  "file": "DIR/Inputs/relative_directory_input1.cpp"
+},
+{
+  "directory": "DIR/Inputs",
+  "command": "clang -E relative_directory_input2.cpp -I.",
+  "file": "DIR/Inputs/relative_directory_input2.cpp"
+}
+]
Index: clang/test/ClangScanDeps/relative_directory.cpp
===================================================================
--- /dev/null
+++ clang/test/ClangScanDeps/relative_directory.cpp
@@ -0,0 +1,25 @@
+// RUN: rm -rf %t.dir
+// RUN: rm -rf %t.cdb
+// RUN: mkdir -p %t.dir
+// RUN: mkdir %t.dir/Inputs
+// RUN: cp %s %t.dir/Inputs/relative_directory_input1.cpp
+// RUN: cp %s %t.dir/Inputs/relative_directory_input2.cpp
+// RUN: touch %t.dir/Inputs/header.h
+// RUN: sed -e "s|DIR|%/t.dir|g" %S/Inputs/relative_directory.json > %t.cdb
+//
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 1 | FileCheck --check-prefixes=CHECK1,CHECK2 %s
+
+// The output order is non-deterministic when using more than one thread,
+// so check the output using two runs.
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 2 | FileCheck --check-prefix=CHECK1 %s
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 2 | FileCheck --check-prefix=CHECK2 %s
+
+#include <header.h>
+
+// CHECK1: relative_directory_input1.o:
+// CHECK1-NEXT: relative_directory_input1.cpp
+// CHECK1-NEXT: header.h
+
+// CHECK2: relative_directory_input2.o:
+// CHECK2-NEXT: relative_directory_input2.cpp
+// CHECK2-NEXT: header.h