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
@@ -36,6 +36,8 @@
       llvm::sys::path::remove_dots(CanonPath, /*remove_dot_dot=*/true);
       C.handleFileDependency(*Opts, CanonPath);
     }
+    for (const auto& ExtraDep : Opts->ExtraDeps)
+      C.handleFileDependency(*Opts, ExtraDep);
   }
 
 private:
diff --git a/clang/test/ClangScanDeps/Inputs/non-header-dependency.json b/clang/test/ClangScanDeps/Inputs/non-header-dependency.json
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/Inputs/non-header-dependency.json
@@ -0,0 +1,7 @@
+[
+    {
+      "directory": "DIR",
+      "command": "clang -E DIR/non-header-dependency_input.cpp -fsanitize=bounds -fsanitize-blacklist=DIR/Inputs/sanitize-blacklist.txt",
+      "file": "DIR/non-header-dependency_input.cpp"
+    }
+]
diff --git a/clang/test/ClangScanDeps/Inputs/sanitize-blacklist.txt b/clang/test/ClangScanDeps/Inputs/sanitize-blacklist.txt
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/Inputs/sanitize-blacklist.txt
@@ -0,0 +1 @@
+fun:*
diff --git a/clang/test/ClangScanDeps/non-header-dependency.cpp b/clang/test/ClangScanDeps/non-header-dependency.cpp
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/non-header-dependency.cpp
@@ -0,0 +1,14 @@
+// RUN: rm -rf %t.dir
+// RUN: rm -rf %t.cdb
+// RUN: mkdir -p %t.dir
+// RUN: cp %s %t.dir/non-header-dependency_input.cpp
+// RUN: mkdir %t.dir/Inputs
+// RUN: cp %S/Inputs/sanitize-blacklist.txt %t.dir/Inputs/sanitize-blacklist.txt
+// RUN: sed -e "s|DIR|%/t.dir|g" %S/Inputs/non-header-dependency.json > %t.cdb
+//
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 1 | FileCheck %s
+
+#define FOO "foo"
+
+// CHECK: Inputs{{/|\\}}sanitize-blacklist.txt
+// CHECK-NEXT: non-header-dependency_input.cpp
diff --git a/clang/tools/clang-scan-deps/ClangScanDeps.cpp b/clang/tools/clang-scan-deps/ClangScanDeps.cpp
--- a/clang/tools/clang-scan-deps/ClangScanDeps.cpp
+++ b/clang/tools/clang-scan-deps/ClangScanDeps.cpp
@@ -17,6 +17,7 @@
 #include "llvm/Support/Signals.h"
 #include "llvm/Support/Threading.h"
 #include <mutex>
+#include <set>
 #include <thread>
 
 using namespace clang;
@@ -66,7 +67,7 @@
                                 StringRef File) override {
         if (!this->Opts)
           this->Opts = std::make_unique<DependencyOutputOptions>(Opts);
-        Dependencies.push_back(File);
+        Dependencies.insert(File);
       }
 
       void printDependencies(std::string &S) {
@@ -76,7 +77,7 @@
         class DependencyPrinter : public DependencyFileGenerator {
         public:
           DependencyPrinter(DependencyOutputOptions &Opts,
-                            ArrayRef<std::string> Dependencies)
+                            std::set<std::string> &Dependencies)
               : DependencyFileGenerator(Opts) {
             for (const auto &Dep : Dependencies)
               addDependency(Dep);
@@ -94,7 +95,7 @@
 
     private:
       std::unique_ptr<DependencyOutputOptions> Opts;
-      std::vector<std::string> Dependencies;
+      std::set<std::string> Dependencies;
     };
 
     DependencyPrinterConsumer Consumer;