diff --git a/CHANGELOG.md b/CHANGELOG.md
index e6077184f0f3..3d47f0537aa5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Fixes
 
+- `[jest-runtime]` Fix for mocks not working with module name mapper ([#7787](https://github.com/facebook/jest/pull/7787))
 - `[jest-cli]` Break dependency cycle when using Jest programmatically ([#7707](https://github.com/facebook/jest/pull/7707))
 - `[jest-config]` Extract setupFilesAfterEnv from preset ([#7724](https://github.com/facebook/jest/pull/7724))
 
diff --git a/e2e/__tests__/moduleNameMapper.test.js b/e2e/__tests__/moduleNameMapper.test.js
index 969b387372ed..e768af3e48bc 100644
--- a/e2e/__tests__/moduleNameMapper.test.js
+++ b/e2e/__tests__/moduleNameMapper.test.js
@@ -7,7 +7,7 @@
  * @flow
  */
 
-import runJest from '../runJest';
+import runJest, {json as runWithJson} from '../runJest';
 import {extractSummary} from '../Utils';
 import {wrap} from 'jest-snapshot-serializer-raw';
 
@@ -28,3 +28,9 @@ test('moduleNameMapper correct configuration', () => {
   expect(status).toBe(0);
   expect(wrap(rest)).toMatchSnapshot();
 });
+
+test('moduleNameMapper with mocking', () => {
+  const {json} = runWithJson('module-name-mapper-mock');
+  expect(json.numTotalTests).toBe(2);
+  expect(json.success).toBe(true);
+});
diff --git a/e2e/module-name-mapper-mock/__tests__/storage/track/Track.test.js b/e2e/module-name-mapper-mock/__tests__/storage/track/Track.test.js
new file mode 100644
index 000000000000..2a1737478788
--- /dev/null
+++ b/e2e/module-name-mapper-mock/__tests__/storage/track/Track.test.js
@@ -0,0 +1,14 @@
+/**
+ * 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.
+ */
+
+const {Track} = require('../../../src/storage/track/Track');
+jest.mock('@@storage/track/Track');
+
+test('relative import', () => {
+  const track = new Track();
+  expect(track.someRandomFunction).not.toBeCalled();
+});
diff --git a/e2e/module-name-mapper-mock/__tests__/storage/track/TrackExpected.test.js b/e2e/module-name-mapper-mock/__tests__/storage/track/TrackExpected.test.js
new file mode 100644
index 000000000000..86224f67fe7d
--- /dev/null
+++ b/e2e/module-name-mapper-mock/__tests__/storage/track/TrackExpected.test.js
@@ -0,0 +1,14 @@
+/**
+ * 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.
+ */
+
+const {Track} = require('@@storage/track/Track');
+jest.mock('@@storage/track/Track');
+
+test('through moduleNameMapper', () => {
+  const track = new Track();
+  expect(track.someRandomFunction).not.toBeCalled();
+});
diff --git a/e2e/module-name-mapper-mock/package.json b/e2e/module-name-mapper-mock/package.json
new file mode 100644
index 000000000000..8a7b6db67be1
--- /dev/null
+++ b/e2e/module-name-mapper-mock/package.json
@@ -0,0 +1,8 @@
+{
+  "jest": {
+    "moduleNameMapper": {
+      "^@@storage/(.*)$": "<rootDir>/src/storage/$1"
+    },
+    "testEnvironment": "node"
+  }
+}
diff --git a/e2e/module-name-mapper-mock/src/storage/track/Track.js b/e2e/module-name-mapper-mock/src/storage/track/Track.js
new file mode 100644
index 000000000000..e91d9a9b047b
--- /dev/null
+++ b/e2e/module-name-mapper-mock/src/storage/track/Track.js
@@ -0,0 +1,12 @@
+/**
+ * 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.
+ */
+
+module.exports.Track = class Track {
+  someRandomFunction() {
+    return 42;
+  }
+};
diff --git a/packages/jest-resolve/src/index.js b/packages/jest-resolve/src/index.js
index 94784e8c0b51..dd9feb66cea7 100644
--- a/packages/jest-resolve/src/index.js
+++ b/packages/jest-resolve/src/index.js
@@ -251,7 +251,7 @@ class Resolver {
     if (mock) {
       return mock;
     } else {
-      const moduleName = this._resolveStubModuleName(from, name);
+      const moduleName = this.resolveStubModuleName(from, name);
       if (moduleName) {
         return this.getModule(moduleName) || moduleName;
       }
@@ -340,7 +340,7 @@ class Resolver {
     );
   }
 
-  _resolveStubModuleName(from: Path, moduleName: string): ?Path {
+  resolveStubModuleName(from: Path, moduleName: string): ?Path {
     const dirname = path.dirname(from);
     const paths = this._options.modulePaths;
     const extensions = this._options.extensions.slice();
diff --git a/packages/jest-runtime/src/__tests__/runtime_gen_mock_from_module.test.js b/packages/jest-runtime/src/__tests__/runtime_gen_mock_from_module.test.js
index d76898b32d27..818b87eaec97 100644
--- a/packages/jest-runtime/src/__tests__/runtime_gen_mock_from_module.test.js
+++ b/packages/jest-runtime/src/__tests__/runtime_gen_mock_from_module.test.js
@@ -10,6 +10,10 @@
 
 let createRuntime;
 
+const moduleNameMapper = {
+  'module/name/(.*)': '<rootDir>/mapped_module_$1.js',
+};
+
 describe('Runtime', () => {
   beforeEach(() => {
     createRuntime = require('createRuntime');
@@ -35,6 +39,16 @@ describe('Runtime', () => {
         expect(mock.fn()).toBe(undefined);
         expect(module.getModuleStateValue()).toBe(origModuleStateValue);
       }));
+
+    it('resolves mapped modules correctly', () =>
+      createRuntime(__filename, {moduleNameMapper}).then(runtime => {
+        const root = runtime.requireModule(runtime.__mockRootPath);
+        const mockModule = root.jest.genMockFromModule(
+          'module/name/genMockFromModule',
+        );
+
+        expect(mockModule.test.mock).toBeTruthy();
+      }));
   });
 
   it('creates mock objects in the right environment', () =>
diff --git a/packages/jest-runtime/src/__tests__/test_root/mapped_module_genMockFromModule.js b/packages/jest-runtime/src/__tests__/test_root/mapped_module_genMockFromModule.js
new file mode 100644
index 000000000000..9e23e5b26b30
--- /dev/null
+++ b/packages/jest-runtime/src/__tests__/test_root/mapped_module_genMockFromModule.js
@@ -0,0 +1,10 @@
+/**
+ * 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.
+ */
+
+module.exports = {
+  test: () => '42',
+};
diff --git a/packages/jest-runtime/src/index.js b/packages/jest-runtime/src/index.js
index 7c69e5925152..806926f45025 100644
--- a/packages/jest-runtime/src/index.js
+++ b/packages/jest-runtime/src/index.js
@@ -389,37 +389,43 @@ class Runtime {
       return (mockRegistry[moduleID] = this._mockFactories[moduleID]());
     }
 
-    let manualMock = this._resolver.getMockModule(from, moduleName);
+    const manualMockOrStub = this._resolver.getMockModule(from, moduleName);
     let modulePath;
-    if (manualMock) {
-      modulePath = this._resolveModule(from, manualMock);
+    if (manualMockOrStub) {
+      modulePath = this._resolveModule(from, manualMockOrStub);
     } else {
       modulePath = this._resolveModule(from, moduleName);
     }
-    // If the actual module file has a __mocks__ dir sitting immediately next
-    // to it, look to see if there is a manual mock for this file.
-    //
-    // subDir1/my_module.js
-    // subDir1/__mocks__/my_module.js
-    // subDir2/my_module.js
-    // subDir2/__mocks__/my_module.js
-    //
-    // Where some other module does a relative require into each of the
-    // respective subDir{1,2} directories and expects a manual mock
-    // corresponding to that particular my_module.js file.
-    const moduleDir = path.dirname(modulePath);
-    const moduleFileName = path.basename(modulePath);
-    const potentialManualMock = path.join(
-      moduleDir,
-      '__mocks__',
-      moduleFileName,
-    );
-    if (fs.existsSync(potentialManualMock)) {
-      manualMock = true;
-      modulePath = potentialManualMock;
-    }
 
-    if (manualMock) {
+    let isManualMock =
+      manualMockOrStub &&
+      !this._resolver.resolveStubModuleName(from, moduleName);
+    if (!isManualMock) {
+      // If the actual module file has a __mocks__ dir sitting immediately next
+      // to it, look to see if there is a manual mock for this file.
+      //
+      // subDir1/my_module.js
+      // subDir1/__mocks__/my_module.js
+      // subDir2/my_module.js
+      // subDir2/__mocks__/my_module.js
+      //
+      // Where some other module does a relative require into each of the
+      // respective subDir{1,2} directories and expects a manual mock
+      // corresponding to that particular my_module.js file.
+
+      const moduleDir = path.dirname(modulePath);
+      const moduleFileName = path.basename(modulePath);
+      const potentialManualMock = path.join(
+        moduleDir,
+        '__mocks__',
+        moduleFileName,
+      );
+      if (fs.existsSync(potentialManualMock)) {
+        isManualMock = true;
+        modulePath = potentialManualMock;
+      }
+    }
+    if (isManualMock) {
       const localModule: Module = {
         children: [],
         exports: {},
@@ -741,8 +747,9 @@ class Runtime {
   }
 
   _generateMock(from: Path, moduleName: string) {
-    const modulePath = this._resolveModule(from, moduleName);
-
+    const modulePath =
+      this._resolver.resolveStubModuleName(from, moduleName) ||
+      this._resolveModule(from, moduleName);
     if (!(modulePath in this._mockMetaDataCache)) {
       // This allows us to handle circular dependencies while generating an
       // automock