diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc2f6c048665..87a9e3f28eaa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,8 @@
   issue. ([#4669](https://github.com/facebook/jest/pull/4669))
 * `[jest-cli]` Fix `--onlyChanged` path case sensitivity on Windows platform
   ([#4730](https://github.com/facebook/jest/pull/4730))
+* `[jest-runtime]` Use realpath to match transformers
+  ([#5000](https://github.com/facebook/jest/pull/5000))
 
 ### Features
 
diff --git a/integration_tests/__tests__/transform-linked-modules.test.js b/integration_tests/__tests__/transform-linked-modules.test.js
new file mode 100644
index 000000000000..fe257ad3eb45
--- /dev/null
+++ b/integration_tests/__tests__/transform-linked-modules.test.js
@@ -0,0 +1,12 @@
+// @flow
+
+'use strict';
+
+const runJest = require('../runJest');
+
+it('should transform linked modules', () => {
+  const result = runJest.json('transform-linked-modules', ['--no-cache']).json;
+
+  expect(result.success).toBe(true);
+  expect(result.numTotalTests).toBe(2);
+});
diff --git a/integration_tests/transform-linked-modules/__tests__/linked-modules.test.js b/integration_tests/transform-linked-modules/__tests__/linked-modules.test.js
new file mode 100644
index 000000000000..0b8930cffccc
--- /dev/null
+++ b/integration_tests/transform-linked-modules/__tests__/linked-modules.test.js
@@ -0,0 +1,9 @@
+test('normal file', () => {
+  const normal = require('../ignored/normal');
+  expect(normal).toEqual('ignored/normal');
+});
+
+test('symlink', () => {
+  const symlink = require('../ignored/symlink');
+  expect(symlink).toEqual('transformed');
+});
diff --git a/integration_tests/transform-linked-modules/ignored/normal.js b/integration_tests/transform-linked-modules/ignored/normal.js
new file mode 100644
index 000000000000..d2135611e150
--- /dev/null
+++ b/integration_tests/transform-linked-modules/ignored/normal.js
@@ -0,0 +1 @@
+module.exports = 'ignored/normal';
diff --git a/integration_tests/transform-linked-modules/ignored/symlink.js b/integration_tests/transform-linked-modules/ignored/symlink.js
new file mode 120000
index 000000000000..296e29907920
--- /dev/null
+++ b/integration_tests/transform-linked-modules/ignored/symlink.js
@@ -0,0 +1 @@
+../package/index.js
\ No newline at end of file
diff --git a/integration_tests/transform-linked-modules/package.json b/integration_tests/transform-linked-modules/package.json
new file mode 100644
index 000000000000..0887a1756750
--- /dev/null
+++ b/integration_tests/transform-linked-modules/package.json
@@ -0,0 +1,13 @@
+{
+  "jest": {
+    "testEnvironment": "node",
+    "transformIgnorePatterns": [
+      "/node_modules/",
+      "<rootDir>/__tests__",
+      "<rootDir>/ignored/"
+    ],
+    "transform": {
+      "^.+\\.js$": "<rootDir>/preprocessor.js"
+    }
+  }
+}
diff --git a/integration_tests/transform-linked-modules/package/index.js b/integration_tests/transform-linked-modules/package/index.js
new file mode 100644
index 000000000000..e2717257ce1d
--- /dev/null
+++ b/integration_tests/transform-linked-modules/package/index.js
@@ -0,0 +1 @@
+module.exports = 'package/index';
diff --git a/integration_tests/transform-linked-modules/preprocessor.js b/integration_tests/transform-linked-modules/preprocessor.js
new file mode 100644
index 000000000000..26d81a441699
--- /dev/null
+++ b/integration_tests/transform-linked-modules/preprocessor.js
@@ -0,0 +1,5 @@
+module.exports = {
+  process() {
+    return 'module.exports = "transformed"';
+  },
+};
diff --git a/packages/jest-runtime/src/script_transformer.js b/packages/jest-runtime/src/script_transformer.js
index 0c97ea28f935..cd7e29aacdeb 100644
--- a/packages/jest-runtime/src/script_transformer.js
+++ b/packages/jest-runtime/src/script_transformer.js
@@ -182,12 +182,22 @@ export default class ScriptTransformer {
     }).code;
   }
 
+  _getRealPath(filepath: Path): Path {
+    try {
+      // $FlowFixMe
+      return process.binding('fs').realpath(filepath) || filepath;
+    } catch (err) {
+      return filepath;
+    }
+  }
+
   transformSource(
-    filename: Path,
+    filepath: Path,
     content: string,
     instrument: boolean,
     mapCoverage: boolean,
   ) {
+    const filename = this._getRealPath(filepath);
     const transform = this._getTransformer(filename);
     const cacheFilePath = this._getFileCachePath(
       filename,