diff --git a/CHANGELOG.md b/CHANGELOG.md
index b706156bc4b3..3b352910144f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Fixes
 
 - `[jest-runtime]` Ensure absolute paths can be resolved within test modules ([11943](https://github.com/facebook/jest/pull/11943))
+- `[jest-runtime]` Use `typeof` assertion instead of `instanceof` to differentiate ModernFakeTimers and LegacyFakeTimers methods ([#11946](https://github.com/facebook/jest/pull/11946))
 
 ### Chore & Maintenance
 
diff --git a/packages/jest-runtime/src/index.ts b/packages/jest-runtime/src/index.ts
index ffe5bc4a64aa..4c308010b30d 100644
--- a/packages/jest-runtime/src/index.ts
+++ b/packages/jest-runtime/src/index.ts
@@ -30,7 +30,7 @@ import type {
   Module,
   ModuleWrapper,
 } from '@jest/environment';
-import {LegacyFakeTimers, ModernFakeTimers} from '@jest/fake-timers';
+import type {LegacyFakeTimers, ModernFakeTimers} from '@jest/fake-timers';
 import type * as JestGlobals from '@jest/globals';
 import type {SourceMapRegistry} from '@jest/source-map';
 import type {RuntimeTransformResult, V8CoverageResult} from '@jest/test-result';
@@ -1961,8 +1961,11 @@ export default class Runtime {
       getRealSystemTime: () => {
         const fakeTimers = _getFakeTimers();
 
-        if (fakeTimers instanceof ModernFakeTimers) {
-          return fakeTimers.getRealSystemTime();
+        if (
+          typeof (fakeTimers as ModernFakeTimers).getRealSystemTime ===
+          'function'
+        ) {
+          return (fakeTimers as ModernFakeTimers).getRealSystemTime();
         } else {
           throw new TypeError(
             'getRealSystemTime is not available when not using modern timers',
@@ -1982,8 +1985,11 @@ export default class Runtime {
       runAllImmediates: () => {
         const fakeTimers = _getFakeTimers();
 
-        if (fakeTimers instanceof LegacyFakeTimers) {
-          fakeTimers.runAllImmediates();
+        if (
+          typeof (fakeTimers as LegacyFakeTimers<unknown>).runAllImmediates ===
+          'function'
+        ) {
+          (fakeTimers as LegacyFakeTimers<unknown>).runAllImmediates();
         } else {
           throw new TypeError(
             'runAllImmediates is not available when using modern timers',
@@ -1998,8 +2004,10 @@ export default class Runtime {
       setSystemTime: (now?: number | Date) => {
         const fakeTimers = _getFakeTimers();
 
-        if (fakeTimers instanceof ModernFakeTimers) {
-          fakeTimers.setSystemTime(now);
+        if (
+          typeof (fakeTimers as ModernFakeTimers).setSystemTime === 'function'
+        ) {
+          (fakeTimers as ModernFakeTimers).setSystemTime(now);
         } else {
           throw new TypeError(
             'setSystemTime is not available when not using modern timers',