diff --git a/packages/babel-preset-react-app/index.js b/packages/babel-preset-react-app/index.js
index 089c81dbbe0..c8f20dde61d 100644
--- a/packages/babel-preset-react-app/index.js
+++ b/packages/babel-preset-react-app/index.js
@@ -8,8 +8,6 @@
  */
 'use strict';
 
-var path = require('path');
-
 const plugins = [
   // class { handleClick = () => { } }
   require.resolve('babel-plugin-transform-class-properties'),
@@ -36,8 +34,6 @@ const plugins = [
       helpers: false,
       polyfill: false,
       regenerator: true,
-      // Resolve the Babel runtime relative to the config.
-      moduleName: path.dirname(require.resolve('babel-runtime/package')),
     },
   ],
 ];
diff --git a/packages/babel-preset-react-app/package.json b/packages/babel-preset-react-app/package.json
index f16cc8dc5f2..175b7b1297f 100644
--- a/packages/babel-preset-react-app/package.json
+++ b/packages/babel-preset-react-app/package.json
@@ -22,7 +22,9 @@
     "babel-plugin-transform-regenerator": "6.24.1",
     "babel-plugin-transform-runtime": "6.23.0",
     "babel-preset-env": "1.4.0",
-    "babel-preset-react": "6.24.1",
-    "babel-runtime": "6.23.0"
+    "babel-preset-react": "6.24.1"
+  },
+  "peerDependencies": {
+    "babel-runtime": "^6.23.0"
   }
 }
diff --git a/packages/react-scripts/config/webpack.config.dev.js b/packages/react-scripts/config/webpack.config.dev.js
index 110968b596d..f34517c0239 100644
--- a/packages/react-scripts/config/webpack.config.dev.js
+++ b/packages/react-scripts/config/webpack.config.dev.js
@@ -93,6 +93,15 @@ module.exports = {
     // https://github.com/facebookincubator/create-react-app/issues/290
     extensions: ['.js', '.json', '.jsx'],
     alias: {
+      // @remove-on-eject-begin
+      // Resolve Babel runtime relative to react-scripts.
+      // It usually still works on npm 3 without this but it would be
+      // unfortunate to rely on, as react-scripts could be symlinked,
+      // and thus babel-runtime might not be resolvable from the source.
+      'babel-runtime': path.dirname(
+        require.resolve('babel-runtime/package.json')
+      ),
+      // @remove-on-eject-end
       // Support React Native Web
       // https://www.smashingmagazine.com/2016/08/a-glimpse-into-the-future-with-react-native-for-web/
       'react-native': 'react-native-web',
diff --git a/packages/react-scripts/config/webpack.config.prod.js b/packages/react-scripts/config/webpack.config.prod.js
index ce9ac5f9523..3dc88d296cd 100644
--- a/packages/react-scripts/config/webpack.config.prod.js
+++ b/packages/react-scripts/config/webpack.config.prod.js
@@ -90,6 +90,15 @@ module.exports = {
     // https://github.com/facebookincubator/create-react-app/issues/290
     extensions: ['.js', '.json', '.jsx'],
     alias: {
+      // @remove-on-eject-begin
+      // Resolve Babel runtime relative to react-scripts.
+      // It usually still works on npm 3 without this but it would be
+      // unfortunate to rely on, as react-scripts could be symlinked,
+      // and thus babel-runtime might not be resolvable from the source.
+      'babel-runtime': path.dirname(
+        require.resolve('babel-runtime/package.json')
+      ),
+      // @remove-on-eject-end
       // Support React Native Web
       // https://www.smashingmagazine.com/2016/08/a-glimpse-into-the-future-with-react-native-for-web/
       'react-native': 'react-native-web',