Index: clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
===================================================================
--- clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -58,11 +58,47 @@
   }
 
   std::error_code setCurrentWorkingDirectory(const Twine &Path) override {
+    assert(llvm::sys::path::is_absolute(Path) && "relative CWD");
     CWD = Path.str();
     return {};
   }
 
+  // Provide absolute paths to the underlying FS, to prevent it from using
+  // the system's CWD.
+  llvm::ErrorOr<llvm::vfs::Status> status(const Twine &Path) override {
+    SmallString<256> Storage;
+    return ProxyFileSystem::status(adjustPath(Path, Storage));
+  }
+
+  llvm::ErrorOr<std::unique_ptr<llvm::vfs::File>>
+  openFileForRead(const Twine &Path) override {
+    SmallString<256> Storage;
+    return ProxyFileSystem::openFileForRead(adjustPath(Path, Storage));
+  }
+  llvm::vfs::directory_iterator dir_begin(const Twine &Dir,
+                                          std::error_code &EC) override {
+    SmallString<256> Storage;
+    return ProxyFileSystem::dir_begin(adjustPath(Dir, Storage), EC);
+  }
+  std::error_code getRealPath(const Twine &Path,
+                              SmallVectorImpl<char> &Output) const override {
+    SmallString<256> Storage;
+    return ProxyFileSystem::getRealPath(adjustPath(Path, Storage), Output);
+  }
+  std::error_code isLocal(const Twine &Path, bool &Result) override {
+    SmallString<256> Storage;
+    return ProxyFileSystem::isLocal(adjustPath(Path, Storage), Result);
+  }
+
 private:
+  Twine adjustPath(const Twine &Path, SmallVectorImpl<char> &Storage) const {
+    assert(!CWD.empty() && "empty CWD");
+
+    Path.toVector(Storage);
+    llvm::sys::fs::make_absolute(CWD, Storage);
+    return Storage;
+  }
+
   std::string CWD;
 };
 
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 +1,20 @@
+// 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 %s
+
+#include <header.h>
+
+// CHECK: relative_directory_input1.o:
+// CHECK-NEXT: relative_directory_input1.cpp
+// CHECK-NEXT: header.h
+
+// CHECK: relative_directory_input2.o:
+// CHECK-NEXT: relative_directory_input2.cpp
+// CHECK-NEXT: header.h