diff --git a/.changeset/happy-banks-repeat.md b/.changeset/happy-banks-repeat.md
new file mode 100644
index 00000000000..18d0e1f53bc
--- /dev/null
+++ b/.changeset/happy-banks-repeat.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/query-core': patch
+---
+
+fix: use Object.is instead of === in replaceEqualDeep to correctly handle NaN equality
diff --git a/packages/query-core/src/__tests__/utils.test.tsx b/packages/query-core/src/__tests__/utils.test.tsx
index 9cee1b46424..f70069a3631 100644
--- a/packages/query-core/src/__tests__/utils.test.tsx
+++ b/packages/query-core/src/__tests__/utils.test.tsx
@@ -416,6 +416,22 @@ describe('core/utils', () => {
 
       expect(next).toBe(current)
     })
+
+    it('preserves reference when objects contain NaN', () => {
+      const prev = { value: NaN }
+      const next = { value: NaN }
+      expect(replaceEqualDeep(prev, next)).toBe(prev)
+    })
+
+    it('handles top-level NaN equality', () => {
+      expect(Number.isNaN(replaceEqualDeep(NaN, NaN))).toBe(true)
+    })
+
+    it('preserves reference for arrays containing NaN', () => {
+      const prev = [NaN, { a: 1 }]
+      const next = [NaN, { a: 1 }]
+      expect(replaceEqualDeep(prev, next)).toBe(prev)
+    })
   })
 
   describe('matchMutation', () => {
diff --git a/packages/query-core/src/utils.ts b/packages/query-core/src/utils.ts
index b29e8ded456..109d02d11f1 100644
--- a/packages/query-core/src/utils.ts
+++ b/packages/query-core/src/utils.ts
@@ -269,7 +269,7 @@ const hasOwn = Object.prototype.hasOwnProperty
  */
 export function replaceEqualDeep<T>(a: unknown, b: T, depth?: number): T
 export function replaceEqualDeep(a: any, b: any, depth = 0): any {
-  if (a === b) {
+  if (Object.is(a, b)) {
     return a
   }
 
@@ -292,7 +292,7 @@ export function replaceEqualDeep(a: any, b: any, depth = 0): any {
     const aItem = a[key]
     const bItem = b[key]
 
-    if (aItem === bItem) {
+    if (Object.is(aItem, bItem)) {
       copy[key] = aItem
       if (array ? i < aSize : hasOwn.call(a, key)) equalItems++
       continue