diff --git a/packages/babel-core/src/transformation/normalize-opts.js b/packages/babel-core/src/transformation/normalize-opts.js
index 4c53b7aa3517..d4a91d83acc6 100644
--- a/packages/babel-core/src/transformation/normalize-opts.js
+++ b/packages/babel-core/src/transformation/normalize-opts.js
@@ -3,21 +3,48 @@
 import path from "path";
 import type { ResolvedConfig } from "../config";
 
+function normalizePath(filepath: string) {
+  return filepath && filepath.replace(/\\/g, "/");
+}
+
+function pickMap(obj, keys, fn) {
+  const res = {};
+  for (const k of keys) res[k] = fn(obj[k]);
+  return res;
+}
+
 export default function normalizeOptions(config: ResolvedConfig): {} {
+  const normalizedPaths = pickMap(
+    config.options,
+    [
+      "filename",
+      "cwd",
+      "filenameRelative",
+      "moduleRoot",
+      "sourceRoot",
+      "sourceFileName",
+    ],
+    normalizePath,
+  );
+
   const {
     filename,
     cwd,
+
     filenameRelative = typeof filename === "string"
-      ? path.relative(cwd, filename)
+      ? path.posix.relative(cwd, filename)
       : "unknown",
-    sourceType = "module",
-    inputSourceMap,
-    sourceMaps = !!inputSourceMap,
 
     moduleRoot,
     sourceRoot = moduleRoot,
 
     sourceFileName = path.basename(filenameRelative),
+  } = normalizedPaths;
+
+  const {
+    sourceType = "module",
+    inputSourceMap,
+    sourceMaps = !!inputSourceMap,
 
     comments = true,
     compact = "auto",
@@ -27,6 +54,7 @@ export default function normalizeOptions(config: ResolvedConfig): {} {
 
   const options = {
     ...opts,
+    ...normalizedPaths,
 
     parserOpts: {
       sourceType:
@@ -39,7 +67,7 @@ export default function normalizeOptions(config: ResolvedConfig): {} {
 
     generatorOpts: {
       // General generator flags.
-      filename,
+      filename: filename,
 
       auxiliaryCommentBefore: opts.auxiliaryCommentBefore,
       auxiliaryCommentAfter: opts.auxiliaryCommentAfter,