diff --git a/packages/babel-plugin-transform-runtime/src/index.js b/packages/babel-plugin-transform-runtime/src/index.js
index 757ec333a461..f53fd16a0be7 100644
--- a/packages/babel-plugin-transform-runtime/src/index.js
+++ b/packages/babel-plugin-transform-runtime/src/index.js
@@ -107,7 +107,6 @@ export default declare((api, options, dirname) => {
     );
   }
 
-  const helpersDir = useESModules ? "helpers/esm" : "helpers";
   const injectCoreJS2 = `${corejsVersion}` === "2";
   const moduleName = injectCoreJS2
     ? "@babel/runtime-corejs2"
@@ -145,6 +144,11 @@ export default declare((api, options, dirname) => {
           const blockHoist =
             isInteropHelper && !isModule(file.path) ? 4 : undefined;
 
+          const helpersDir =
+            useESModules && file.path.node.sourceType === "module"
+              ? "helpers/esm"
+              : "helpers";
+
           return this.addDefaultImport(
             `${modulePath}/${helpersDir}/${name}`,
             name,
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/input.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/input.mjs
similarity index 100%
rename from packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/input.js
rename to packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/input.mjs
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.js
deleted file mode 100644
index fd691a2742a1..000000000000
--- a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.js
+++ /dev/null
@@ -1,23 +0,0 @@
-var _classCallCheck = require("@babel/runtime-corejs2/helpers/esm/classCallCheck");
-
-var _possibleConstructorReturn = require("@babel/runtime-corejs2/helpers/esm/possibleConstructorReturn");
-
-var _getPrototypeOf = require("@babel/runtime-corejs2/helpers/esm/getPrototypeOf");
-
-var _inherits = require("@babel/runtime-corejs2/helpers/esm/inherits");
-
-let Foo =
-/*#__PURE__*/
-function (_Bar) {
-  "use strict";
-
-  _inherits(Foo, _Bar);
-
-  function Foo() {
-    _classCallCheck(this, Foo);
-
-    return _possibleConstructorReturn(this, _getPrototypeOf(Foo).apply(this, arguments));
-  }
-
-  return Foo;
-}(Bar);
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.mjs b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.mjs
new file mode 100644
index 000000000000..828c9aa787ef
--- /dev/null
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs-useES6Modules/output.mjs
@@ -0,0 +1,18 @@
+import _classCallCheck from "@babel/runtime-corejs2/helpers/esm/classCallCheck";
+import _possibleConstructorReturn from "@babel/runtime-corejs2/helpers/esm/possibleConstructorReturn";
+import _getPrototypeOf from "@babel/runtime-corejs2/helpers/esm/getPrototypeOf";
+import _inherits from "@babel/runtime-corejs2/helpers/esm/inherits";
+
+let Foo =
+/*#__PURE__*/
+function (_Bar) {
+  _inherits(Foo, _Bar);
+
+  function Foo() {
+    _classCallCheck(this, Foo);
+
+    return _possibleConstructorReturn(this, _getPrototypeOf(Foo).apply(this, arguments));
+  }
+
+  return Foo;
+}(Bar);
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/input.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/input.mjs
similarity index 100%
rename from packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/input.js
rename to packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/input.mjs
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.js
deleted file mode 100644
index 91eb87aa1694..000000000000
--- a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.js
+++ /dev/null
@@ -1,23 +0,0 @@
-var _classCallCheck = require("@babel/runtime-corejs2/helpers/classCallCheck");
-
-var _possibleConstructorReturn = require("@babel/runtime-corejs2/helpers/possibleConstructorReturn");
-
-var _getPrototypeOf = require("@babel/runtime-corejs2/helpers/getPrototypeOf");
-
-var _inherits = require("@babel/runtime-corejs2/helpers/inherits");
-
-let Foo =
-/*#__PURE__*/
-function (_Bar) {
-  "use strict";
-
-  _inherits(Foo, _Bar);
-
-  function Foo() {
-    _classCallCheck(this, Foo);
-
-    return _possibleConstructorReturn(this, _getPrototypeOf(Foo).apply(this, arguments));
-  }
-
-  return Foo;
-}(Bar);
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.mjs b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.mjs
new file mode 100644
index 000000000000..44f4d72a0409
--- /dev/null
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/corejs/output.mjs
@@ -0,0 +1,18 @@
+import _classCallCheck from "@babel/runtime-corejs2/helpers/classCallCheck";
+import _possibleConstructorReturn from "@babel/runtime-corejs2/helpers/possibleConstructorReturn";
+import _getPrototypeOf from "@babel/runtime-corejs2/helpers/getPrototypeOf";
+import _inherits from "@babel/runtime-corejs2/helpers/inherits";
+
+let Foo =
+/*#__PURE__*/
+function (_Bar) {
+  _inherits(Foo, _Bar);
+
+  function Foo() {
+    _classCallCheck(this, Foo);
+
+    return _possibleConstructorReturn(this, _getPrototypeOf(Foo).apply(this, arguments));
+  }
+
+  return Foo;
+}(Bar);
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/input.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/input.js
similarity index 100%
rename from packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/input.js
rename to packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/input.js
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/options.json b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/options.json
similarity index 100%
rename from packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/options.json
rename to packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/options.json
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/output.js b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/output.js
similarity index 56%
rename from packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/output.js
rename to packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/output.js
index d2863837c42b..39882dcd466a 100644
--- a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules/output.js
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-cjs/output.js
@@ -1,10 +1,10 @@
-var _classCallCheck = require("@babel/runtime/helpers/esm/classCallCheck");
+var _classCallCheck = require("@babel/runtime/helpers/classCallCheck");
 
-var _possibleConstructorReturn = require("@babel/runtime/helpers/esm/possibleConstructorReturn");
+var _possibleConstructorReturn = require("@babel/runtime/helpers/possibleConstructorReturn");
 
-var _getPrototypeOf = require("@babel/runtime/helpers/esm/getPrototypeOf");
+var _getPrototypeOf = require("@babel/runtime/helpers/getPrototypeOf");
 
-var _inherits = require("@babel/runtime/helpers/esm/inherits");
+var _inherits = require("@babel/runtime/helpers/inherits");
 
 let Foo =
 /*#__PURE__*/
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/input.mjs b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/input.mjs
new file mode 100644
index 000000000000..dcde0c7bf9a2
--- /dev/null
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/input.mjs
@@ -0,0 +1 @@
+class Foo extends Bar {}
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/options.json b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/options.json
new file mode 100644
index 000000000000..92d77833b5a7
--- /dev/null
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/options.json
@@ -0,0 +1,3 @@
+{
+  "plugins": [["transform-runtime", { "useESModules": true }], "transform-classes"]
+}
diff --git a/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/output.mjs b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/output.mjs
new file mode 100644
index 000000000000..0247fa0b5556
--- /dev/null
+++ b/packages/babel-plugin-transform-runtime/test/fixtures/use-options/useESModules-mjs/output.mjs
@@ -0,0 +1,18 @@
+import _classCallCheck from "@babel/runtime/helpers/esm/classCallCheck";
+import _possibleConstructorReturn from "@babel/runtime/helpers/esm/possibleConstructorReturn";
+import _getPrototypeOf from "@babel/runtime/helpers/esm/getPrototypeOf";
+import _inherits from "@babel/runtime/helpers/esm/inherits";
+
+let Foo =
+/*#__PURE__*/
+function (_Bar) {
+  _inherits(Foo, _Bar);
+
+  function Foo() {
+    _classCallCheck(this, Foo);
+
+    return _possibleConstructorReturn(this, _getPrototypeOf(Foo).apply(this, arguments));
+  }
+
+  return Foo;
+}(Bar);