diff --git a/.changeset/atom-set-undefined.md b/.changeset/atom-set-undefined.md
new file mode 100644
index 00000000..cdaab220
--- /dev/null
+++ b/.changeset/atom-set-undefined.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/store': patch
+---
+
+Fix `atom.set(undefined)` being ignored. A mutable atom now takes `undefined` as its new value and compares it like any other, so setting `undefined` again does not notify subscribers. Only an internal `_update()` call made with no argument is still skipped.
diff --git a/packages/store/src/atom.ts b/packages/store/src/atom.ts
index 1a29e607..be69b62e 100644
--- a/packages/store/src/atom.ts
+++ b/packages/store/src/atom.ts
@@ -203,9 +203,10 @@ export function createAtom<T>(
         activeSub = atom
         ++cycle
         atom.depsTail = undefined
-      } else if (getValue === undefined) {
+      } else if (arguments.length === 0) {
         // Mutable atoms can be marked dirty by the reactive graph, but they should
-        // never be recomputed without an explicit value/updater.
+        // never be recomputed without an explicit value/updater. Check the argument
+        // count rather than `undefined`, which `set(undefined)` passes as a value.
         return false
       }
       if (isComputed) {
@@ -219,7 +220,12 @@ export function createAtom<T>(
             : getValue === undefined && isComputed
               ? getter(oldValue)
               : getValue!
-        if (oldValue === undefined || !compare(oldValue, newValue)) {
+        // A computed atom treats an `undefined` snapshot as not computed yet. A
+        // mutable atom's `undefined` is a value like any other.
+        if (
+          (isComputed && oldValue === undefined) ||
+          !compare(oldValue, newValue)
+        ) {
           atom._snapshot = newValue
           return true
         }
diff --git a/packages/store/tests/store.test.ts b/packages/store/tests/store.test.ts
index 7c088144..f1b17b1b 100644
--- a/packages/store/tests/store.test.ts
+++ b/packages/store/tests/store.test.ts
@@ -1,6 +1,6 @@
 import { describe, expect, test, vi } from 'vitest'
 // import { Store } from '../src/index'
-import { createStore } from '../src'
+import { createAtom, createStore } from '../src'
 
 describe('store', () => {
   test(`should set the initial value`, () => {
@@ -116,4 +116,17 @@ describe('store', () => {
     expect(atom._update()).toBe(false)
     expect(store.state).toEqual({ pageIndex: 1 })
   })
+
+  test('mutable atom can be set to undefined', () => {
+    const atom = createAtom<number | undefined>(1)
+    const fn = vi.fn()
+    atom.subscribe(fn)
+
+    atom.set(undefined)
+    atom.set(undefined)
+
+    expect(atom.get()).toBeUndefined()
+    expect(fn).toHaveBeenCalledTimes(1)
+    expect(fn).toHaveBeenCalledWith(undefined)
+  })
 })