diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e9c4c1ef83f..34ea80f615cd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -94,7 +94,9 @@
 * `[jest-util]` Fix handling of NaN/Infinity in mock timer delay
   ([#5966](https://github.com/facebook/jest/pull/5966))
 * `[jest-resolve]` Generalise test for package main entries equivalent to ".".
-  ([#5968)](https://github.com/facebook/jest/pull/5968)
+  ([#5968](https://github.com/facebook/jest/pull/5968))
+* `[jest-config]` Ensure that custom resolvers are used when resolving the configuration
+  ([#5976](https://github.com/facebook/jest/pull/5976))
 
 ### Chore & Maintenance
 
diff --git a/integration-tests/__tests__/custom-resolver.test.js b/integration-tests/__tests__/custom-resolver.test.js
new file mode 100644
index 000000000000..5e3582ec861f
--- /dev/null
+++ b/integration-tests/__tests__/custom-resolver.test.js
@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. 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.
+ *
+ * @flow
+ */
+'use strict';
+
+const runJest = require('../runJest');
+
+test('use the custom resolver', () => {
+  const result = runJest('custom-resolver');
+  expect(result.status).toBe(0);
+});
diff --git a/integration-tests/custom-resolver/__tests__/custom-resolver.test.js b/integration-tests/custom-resolver/__tests__/custom-resolver.test.js
new file mode 100644
index 000000000000..ac91d1c88fa0
--- /dev/null
+++ b/integration-tests/custom-resolver/__tests__/custom-resolver.test.js
@@ -0,0 +1,11 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. 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';
+
+test('should use the custom resolver', () => {
+  require('foo');
+});
diff --git a/integration-tests/custom-resolver/bar.js b/integration-tests/custom-resolver/bar.js
new file mode 100644
index 000000000000..cc40a4649c9f
--- /dev/null
+++ b/integration-tests/custom-resolver/bar.js
@@ -0,0 +1 @@
+module.exports = () => {};
diff --git a/integration-tests/custom-resolver/foo.js b/integration-tests/custom-resolver/foo.js
new file mode 100644
index 000000000000..cc40a4649c9f
--- /dev/null
+++ b/integration-tests/custom-resolver/foo.js
@@ -0,0 +1 @@
+module.exports = () => {};
diff --git a/integration-tests/custom-resolver/package.json b/integration-tests/custom-resolver/package.json
new file mode 100644
index 000000000000..dd319619f468
--- /dev/null
+++ b/integration-tests/custom-resolver/package.json
@@ -0,0 +1,7 @@
+{
+  "name": "custom-resolver",
+  "jest": {
+    "globalSetup": "foo",
+    "resolver": "./resolver.js"
+  }
+}
diff --git a/integration-tests/custom-resolver/resolver.js b/integration-tests/custom-resolver/resolver.js
new file mode 100644
index 000000000000..0764e575a6e1
--- /dev/null
+++ b/integration-tests/custom-resolver/resolver.js
@@ -0,0 +1,9 @@
+const defaultResolver = require('jest-resolve/build/default_resolver').default;
+
+module.exports = (name, options) => {
+  if (name === 'foo' || name === 'bar') {
+    return `${__dirname}/${name}.js`;
+  } else {
+    return defaultResolver(name, options);
+  }
+};
diff --git a/packages/jest-config/src/normalize.js b/packages/jest-config/src/normalize.js
index 93b3ce7ae6cb..ef07905c3ee6 100644
--- a/packages/jest-config/src/normalize.js
+++ b/packages/jest-config/src/normalize.js
@@ -363,7 +363,21 @@ export default function normalize(options: InitialOptions, argv: Argv) {
   const newOptions = Object.assign({}, DEFAULT_CONFIG);
   // Cast back to exact type
   options = (options: InitialOptions);
+
+  if (options.resolver) {
+    newOptions.resolver = resolve(
+      null,
+      options.rootDir,
+      'resolver',
+      options.resolver,
+    );
+  }
+
   Object.keys(options).reduce((newOptions, key) => {
+    // The resolver has been resolved separately; skip it
+    if (key === 'resolver') {
+      return newOptions;
+    }
     let value;
     switch (key) {
       case 'collectCoverageOnlyFrom':
@@ -373,7 +387,9 @@ export default function normalize(options: InitialOptions, argv: Argv) {
       case 'snapshotSerializers':
         value =
           options[key] &&
-          options[key].map(resolve.bind(null, options.rootDir, key));
+          options[key].map(
+            resolve.bind(null, newOptions.resolver, options.rootDir, key),
+          );
         break;
       case 'modulePaths':
       case 'roots':
@@ -401,12 +417,13 @@ export default function normalize(options: InitialOptions, argv: Argv) {
       case 'globalSetup':
       case 'globalTeardown':
       case 'moduleLoader':
-      case 'resolver':
       case 'runner':
       case 'setupTestFrameworkScriptFile':
       case 'testResultsProcessor':
       case 'testRunner':
-        value = options[key] && resolve(options.rootDir, key, options[key]);
+        value =
+          options[key] &&
+          resolve(newOptions.resolver, options.rootDir, key, options[key]);
         break;
       case 'moduleNameMapper':
         const moduleNameMapper = options[key];
@@ -423,7 +440,12 @@ export default function normalize(options: InitialOptions, argv: Argv) {
           transform &&
           Object.keys(transform).map(regex => [
             regex,
-            resolve(options.rootDir, key, transform[regex]),
+            resolve(
+              newOptions.resolver,
+              options.rootDir,
+              key,
+              transform[regex],
+            ),
           ]);
         break;
       case 'coveragePathIgnorePatterns':
@@ -438,6 +460,7 @@ export default function normalize(options: InitialOptions, argv: Argv) {
         value = Object.assign({}, options[key]);
         if (value.hasteImplModulePath != null) {
           value.hasteImplModulePath = resolve(
+            newOptions.resolver,
             options.rootDir,
             'haste.hasteImplModulePath',
             replaceRootDirInPath(options.rootDir, value.hasteImplModulePath),
@@ -520,7 +543,7 @@ export default function normalize(options: InitialOptions, argv: Argv) {
         break;
       case 'watchPlugins':
         value = (options[key] || []).map(watchPlugin =>
-          resolve(options.rootDir, key, watchPlugin),
+          resolve(newOptions.resolver, options.rootDir, key, watchPlugin),
         );
         break;
     }
diff --git a/packages/jest-config/src/utils.js b/packages/jest-config/src/utils.js
index c85998edbfe4..d31cc17503e3 100644
--- a/packages/jest-config/src/utils.js
+++ b/packages/jest-config/src/utils.js
@@ -28,11 +28,17 @@ const createValidationError = (message: string) => {
   );
 };
 
-export const resolve = (rootDir: string, key: string, filePath: Path) => {
+export const resolve = (
+  resolver: ?string,
+  rootDir: string,
+  key: string,
+  filePath: Path,
+) => {
   const module = Resolver.findNodeModule(
     replaceRootDirInPath(rootDir, filePath),
     {
       basedir: rootDir,
+      resolver,
     },
   );