diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9efb72ecf5a0..09a1d301a013 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -109,6 +109,7 @@
 - `[jest-resolve]` Fix `isBuiltinModule` to support versions of node without `module.builtinModules` ([#7565](https://github.com/facebook/jest/pull/7565))
 - `[babel-jest]` Set `cwd` to be resilient to it changing during the runtime of the tests ([#7574](https://github.com/facebook/jest/pull/7574))
 - `[jest-snapshot]` Write and read snapshots from disk even if `fs` is mocked ([#7080](https://github.com/facebook/jest/pull/7080))
+- `[jest-config]` Normalize `config.cwd` and `config.rootDir` using `realpath ([#7598](https://github.com/facebook/jest/pull/7598))
 
 ### Chore & Maintenance
 
diff --git a/packages/jest-config/package.json b/packages/jest-config/package.json
index b00d0b7c52c7..1088d90fc266 100644
--- a/packages/jest-config/package.json
+++ b/packages/jest-config/package.json
@@ -21,7 +21,8 @@
     "jest-util": "^23.4.0",
     "jest-validate": "^23.6.0",
     "micromatch": "^2.3.11",
-    "pretty-format": "^23.6.0"
+    "pretty-format": "^23.6.0",
+    "realpath-native": "^1.0.2"
   },
   "engines": {
     "node": ">= 6"
diff --git a/packages/jest-config/src/normalize.js b/packages/jest-config/src/normalize.js
index bf1f3bdbd329..e820158e1157 100644
--- a/packages/jest-config/src/normalize.js
+++ b/packages/jest-config/src/normalize.js
@@ -25,6 +25,7 @@ import {clearLine} from 'jest-util';
 import chalk from 'chalk';
 import getMaxWorkers from './getMaxWorkers';
 import micromatch from 'micromatch';
+import {sync as realpath} from 'realpath-native';
 import Resolver from 'jest-resolve';
 import {replacePathSepForRegex} from 'jest-regex-util';
 import {
@@ -288,6 +289,14 @@ const normalizeRootDir = (options: InitialOptions): InitialOptions => {
     );
   }
   options.rootDir = path.normalize(options.rootDir);
+
+  try {
+    // try to resolve windows short paths, ignoring errors (permission errors, mostly)
+    options.rootDir = realpath(options.rootDir);
+  } catch (e) {
+    // ignored
+  }
+
   return options;
 };
 
@@ -442,6 +451,13 @@ export default function normalize(options: InitialOptions, argv: Argv) {
     DefaultOptions & ProjectConfig & GlobalConfig,
   > = (Object.assign({}, DEFAULT_CONFIG): any);
 
+  try {
+    // try to resolve windows short paths, ignoring errors (permission errors, mostly)
+    newOptions.cwd = realpath(newOptions.cwd);
+  } catch (e) {
+    // ignored
+  }
+
   if (options.resolver) {
     newOptions.resolver = resolve(null, {
       filePath: options.resolver,
diff --git a/yarn.lock b/yarn.lock
index b6a123763cf5..170690cb062c 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -11234,7 +11234,7 @@ readdirp@^2.0.0:
     micromatch "^3.1.10"
     readable-stream "^2.0.2"
 
-realpath-native@^1.0.0:
+realpath-native@^1.0.0, realpath-native@^1.0.2:
   version "1.0.2"
   resolved "https://registry.yarnpkg.com/realpath-native/-/realpath-native-1.0.2.tgz#cd51ce089b513b45cf9b1516c82989b51ccc6560"
   integrity sha512-+S3zTvVt9yTntFrBpm7TQmQ3tzpCrnA1a/y+3cUHAc9ZR6aIjG0WNLR+Rj79QpJktY+VeW/TQtFlQ1bzsehI8g==