diff --git a/packages/runtime-core/__tests__/rendererTemplateRef.spec.ts b/packages/runtime-core/__tests__/rendererTemplateRef.spec.ts
index a7ae7a06bfd..ae30878a4fc 100644
--- a/packages/runtime-core/__tests__/rendererTemplateRef.spec.ts
+++ b/packages/runtime-core/__tests__/rendererTemplateRef.spec.ts
@@ -10,6 +10,7 @@ import {
   render,
   serializeInner,
   shallowRef,
+  watch,
 } from '@vue/runtime-test'
 
 describe('api: template refs', () => {
@@ -179,6 +180,51 @@ describe('api: template refs', () => {
     expect(el.value).toBe(null)
   })
 
+  // #12639
+  it('update and unmount child in the same tick', async () => {
+    const root = nodeOps.createElement('div')
+    const el = ref(null)
+    const toggle = ref(true)
+    const show = ref(true)
+
+    const Comp = defineComponent({
+      emits: ['change'],
+      props: ['show'],
+      setup(props, { emit }) {
+        watch(
+          () => props.show,
+          () => {
+            emit('change')
+          },
+        )
+        return () => h('div', 'hi')
+      },
+    })
+
+    const App = {
+      setup() {
+        return {
+          refKey: el,
+        }
+      },
+      render() {
+        return toggle.value
+          ? h(Comp, {
+              ref: 'refKey',
+              show: show.value,
+              onChange: () => (toggle.value = false),
+            })
+          : null
+      },
+    }
+    render(h(App), root)
+    expect(el.value).not.toBe(null)
+
+    show.value = false
+    await nextTick()
+    expect(el.value).toBe(null)
+  })
+
   test('string ref inside slots', async () => {
     const root = nodeOps.createElement('div')
     const spy = vi.fn()
diff --git a/packages/runtime-core/src/rendererTemplateRef.ts b/packages/runtime-core/src/rendererTemplateRef.ts
index ca21030dc35..0e40c9534ca 100644
--- a/packages/runtime-core/src/rendererTemplateRef.ts
+++ b/packages/runtime-core/src/rendererTemplateRef.ts
@@ -13,11 +13,12 @@ import { isAsyncWrapper } from './apiAsyncComponent'
 import { warn } from './warning'
 import { isRef, toRaw } from '@vue/reactivity'
 import { ErrorCodes, callWithErrorHandling } from './errorHandling'
-import type { SchedulerJob } from './scheduler'
+import { type SchedulerJob, SchedulerJobFlags } from './scheduler'
 import { queuePostRenderEffect } from './renderer'
 import { type ComponentOptions, getComponentPublicInstance } from './component'
 import { knownTemplateRefs } from './helpers/useTemplateRef'
 
+const pendingSetRefMap = new WeakMap<VNode, SchedulerJob>()
 /**
  * Function for handling a template ref
  */
@@ -153,9 +154,19 @@ export function setRef(
         // #1789: for non-null values, set them after render
         // null values means this is unmount and it should not overwrite another
         // ref with the same key
-        ;(doSet as SchedulerJob).id = -1
-        queuePostRenderEffect(doSet, parentSuspense)
+        const job: SchedulerJob = () => {
+          doSet()
+          pendingSetRefMap.delete(vnode)
+        }
+        job.id = -1
+        pendingSetRefMap.set(vnode, job)
+        queuePostRenderEffect(job, parentSuspense)
       } else {
+        const pendingSetRef = pendingSetRefMap.get(vnode)
+        if (pendingSetRef) {
+          pendingSetRef.flags! |= SchedulerJobFlags.DISPOSED
+          pendingSetRefMap.delete(vnode)
+        }
         doSet()
       }
     } else if (__DEV__) {