diff --git a/packages/jest-runtime/src/ScriptTransformer.js b/packages/jest-runtime/src/ScriptTransformer.js
index aef3d85022b9..7e1124bbdcf7 100644
--- a/packages/jest-runtime/src/ScriptTransformer.js
+++ b/packages/jest-runtime/src/ScriptTransformer.js
@@ -301,7 +301,7 @@ export default class ScriptTransformer {
     const isInternalModule = !!(options && options.isInternalModule);
     const isCoreModule = !!(options && options.isCoreModule);
     const content = stripShebang(
-      fileSource || fs.readFileSync(filename, 'utf8'),
+      fileSource || fs.readFileSync(filename.split('?')[0], 'utf8'),
     );
 
     let wrappedCode: string;
@@ -513,7 +513,7 @@ const readCacheFile = (cachePath: Path): ?string => {
 };
 
 const getScriptCacheKey = (filename, instrument: boolean) => {
-  const mtime = fs.statSync(filename).mtime;
+  const mtime = fs.statSync(filename.split('?')[0]).mtime;
   return filename + '_' + mtime.getTime() + (instrument ? '_instrumented' : '');
 };
 
diff --git a/packages/jest-runtime/src/index.js b/packages/jest-runtime/src/index.js
index 05dc03a7a35b..030c7a879b37 100644
--- a/packages/jest-runtime/src/index.js
+++ b/packages/jest-runtime/src/index.js
@@ -343,9 +343,9 @@ class Runtime {
         loaded: false,
       };
       moduleRegistry[modulePath] = localModule;
-      if (path.extname(modulePath) === '.json') {
+      if (path.extname(modulePath.split('?')[0]) === '.json') {
         localModule.exports = this._environment.global.JSON.parse(
-          stripBOM(fs.readFileSync(modulePath, 'utf8')),
+          stripBOM(fs.readFileSync(modulePath.split('?')[0], 'utf8')),
         );
       } else if (path.extname(modulePath) === '.node') {
         // $FlowFixMe
@@ -413,7 +413,7 @@ class Runtime {
       '__mocks__',
       moduleFileName,
     );
-    if (fs.existsSync(potentialManualMock)) {
+    if (fs.existsSync(potentialManualMock.split('?')[0])) {
       manualMock = true;
       modulePath = potentialManualMock;
     }
@@ -511,7 +511,7 @@ class Runtime {
       if (
         coveredFiles.has(sourcePath) &&
         this._needsCoverageMapped.has(sourcePath) &&
-        fs.existsSync(this._sourceMapRegistry[sourcePath])
+        fs.existsSync(this._sourceMapRegistry[sourcePath].split('?')[0])
       ) {
         result[sourcePath] = this._sourceMapRegistry[sourcePath];
       }