diff --git a/e2e/__tests__/globalSetup.test.ts b/e2e/__tests__/globalSetup.test.ts
index 4ed55175c4b2..7eacf5830326 100644
--- a/e2e/__tests__/globalSetup.test.ts
+++ b/e2e/__tests__/globalSetup.test.ts
@@ -10,7 +10,7 @@ import fs from 'fs';
 import os from 'os';
 import path from 'path';
 import runJest, {json as runWithJson} from '../runJest';
-import {cleanup} from '../Utils';
+import {cleanup, run} from '../Utils';
 
 const DIR = path.join(os.tmpdir(), 'jest-global-setup');
 const project1DIR = path.join(os.tmpdir(), 'jest-global-setup-project-1');
@@ -19,18 +19,21 @@ const customTransformDIR = path.join(
   os.tmpdir(),
   'jest-global-setup-custom-transform',
 );
+const nodeModulesDIR = path.join(os.tmpdir(), 'jest-global-setup-node-modules');
 
 beforeEach(() => {
   cleanup(DIR);
   cleanup(project1DIR);
   cleanup(project2DIR);
   cleanup(customTransformDIR);
+  cleanup(nodeModulesDIR);
 });
 afterAll(() => {
   cleanup(DIR);
   cleanup(project1DIR);
   cleanup(project2DIR);
   cleanup(customTransformDIR);
+  cleanup(nodeModulesDIR);
 });
 
 test('globalSetup is triggered once before all test suites', () => {
@@ -166,3 +169,12 @@ test('should not transpile the transformer', () => {
 
   expect(status).toBe(0);
 });
+
+test('should transform node_modules if configured by transformIgnorePatterns', () => {
+  const testDir = path.resolve(__dirname, '..', 'global-setup-node-modules');
+  run('yarn', testDir);
+
+  const {status} = runJest('global-setup-node-modules', [`--no-cache`]);
+
+  expect(status).toBe(0);
+});
diff --git a/e2e/global-setup-node-modules/__tests__/test.js b/e2e/global-setup-node-modules/__tests__/test.js
new file mode 100644
index 000000000000..fe1ea73516c9
--- /dev/null
+++ b/e2e/global-setup-node-modules/__tests__/test.js
@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+'use strict';
+
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+
+const DIR = path.join(os.tmpdir(), 'jest-global-setup-node-modules');
+
+test('should exist setup file', () => {
+  const files = fs.readdirSync(DIR);
+  expect(files).toHaveLength(1);
+  const setup = fs.readFileSync(path.join(DIR, files[0]), 'utf8');
+  expect(setup).toBe('setup function');
+});
diff --git a/e2e/global-setup-node-modules/babel.config.js b/e2e/global-setup-node-modules/babel.config.js
new file mode 100644
index 000000000000..f037a1a2a147
--- /dev/null
+++ b/e2e/global-setup-node-modules/babel.config.js
@@ -0,0 +1,12 @@
+module.exports = {
+  presets: [
+    [
+      '@babel/preset-env',
+      {
+        targets: {
+          node: 'current',
+        },
+      },
+    ],
+  ],
+};
diff --git a/e2e/global-setup-node-modules/package.json b/e2e/global-setup-node-modules/package.json
new file mode 100644
index 000000000000..55fb042a9a07
--- /dev/null
+++ b/e2e/global-setup-node-modules/package.json
@@ -0,0 +1,13 @@
+{
+  "devDependencies": {
+    "lodash-es": "^4.17.11"
+  },
+  "jest": {
+    "testEnvironment": "node",
+    "globalSetup": "<rootDir>/setup.js",
+    "transformIgnorePatterns": [
+      "/node_modules/(?!(?:lodash-es)/)",
+      "/packages/"
+    ]
+  }
+}
diff --git a/e2e/global-setup-node-modules/setup.js b/e2e/global-setup-node-modules/setup.js
new file mode 100644
index 000000000000..c0dee9f62cf9
--- /dev/null
+++ b/e2e/global-setup-node-modules/setup.js
@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+import {compact} from 'lodash-es';
+const crypto = require('crypto');
+const fs = require('fs');
+const {createDirectory} = require('jest-util');
+const os = require('os');
+const path = require('path');
+
+const DIR = path.join(os.tmpdir(), 'jest-global-setup-node-modules');
+
+module.exports = function() {
+  return new Promise(resolve => {
+    createDirectory(DIR);
+    const fileId = crypto.randomBytes(20).toString('hex');
+    fs.writeFileSync(path.join(DIR, fileId), `setup ${typeof compact}`);
+    resolve();
+  });
+};
diff --git a/e2e/global-setup-node-modules/yarn.lock b/e2e/global-setup-node-modules/yarn.lock
new file mode 100644
index 000000000000..6febeb67c34b
--- /dev/null
+++ b/e2e/global-setup-node-modules/yarn.lock
@@ -0,0 +1,8 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+lodash-es@^4.17.11:
+  version "4.17.11"
+  resolved "https://registry.yarnpkg.com/lodash-es/-/lodash-es-4.17.11.tgz#145ab4a7ac5c5e52a3531fb4f310255a152b4be0"
+  integrity sha512-DHb1ub+rMjjrxqlB3H56/6MXtm1lSksDp2rA2cNWjG8mlDUYFhUj3Di2Zn5IwSU87xLv8tNIQ7sSwE/YOX/D/Q==
diff --git a/packages/jest-core/src/runGlobalHook.ts b/packages/jest-core/src/runGlobalHook.ts
index 32ba09112ec7..5abfa5101e8c 100644
--- a/packages/jest-core/src/runGlobalHook.ts
+++ b/packages/jest-core/src/runGlobalHook.ts
@@ -60,6 +60,7 @@ export default async ({
           transformer.transformSource(filename, code, false).code || code,
         {
           exts: [extname(modulePath)],
+          ignoreNodeModules: false,
           matcher: transformer.shouldTransform.bind(transformer),
         },
       );