diff --git a/packages/query-core/src/__tests__/queryClient.test.tsx b/packages/query-core/src/__tests__/queryClient.test.tsx
index c09db304467..b34fca2311c 100644
--- a/packages/query-core/src/__tests__/queryClient.test.tsx
+++ b/packages/query-core/src/__tests__/queryClient.test.tsx
@@ -1600,6 +1600,53 @@ describe('queryClient', () => {
       expect(queryFn).toHaveBeenCalledTimes(1)
       unsubscribe()
     })
+
+    // Regression test for https://github.com/TanStack/query/issues/3741
+    it('should match keys with `undefined` properties when ignoreUndefinedInKeys is set', async () => {
+      const queryFnAll = vi.fn().mockReturnValue('all')
+      const queryFnFiltered = vi.fn().mockReturnValue('filtered')
+
+      await queryClient.fetchQuery({
+        queryKey: [{ entity: 'todos', scope: 'list' }],
+        queryFn: queryFnAll,
+      })
+      await queryClient.fetchQuery({
+        queryKey: [{ entity: 'todos', scope: 'list', filter: { done: true } }],
+        queryFn: queryFnFiltered,
+      })
+
+      const observerAll = new QueryObserver(queryClient, {
+        queryKey: [{ entity: 'todos', scope: 'list' }],
+        queryFn: queryFnAll,
+        staleTime: Infinity,
+      })
+      const observerFiltered = new QueryObserver(queryClient, {
+        queryKey: [{ entity: 'todos', scope: 'list', filter: { done: true } }],
+        queryFn: queryFnFiltered,
+        staleTime: Infinity,
+      })
+      const u1 = observerAll.subscribe(() => undefined)
+      const u2 = observerFiltered.subscribe(() => undefined)
+
+      // Without the option: undefined-keyed invalidation only hits the
+      // unfiltered cache entry — the filtered one is NOT refetched.
+      await queryClient.invalidateQueries({
+        queryKey: [{ entity: 'todos', scope: 'list', filter: undefined }],
+      })
+      expect(queryFnAll).toHaveBeenCalledTimes(2)
+      expect(queryFnFiltered).toHaveBeenCalledTimes(1)
+
+      // With the option: undefined property is ignored → both entries match.
+      await queryClient.invalidateQueries({
+        queryKey: [{ entity: 'todos', scope: 'list', filter: undefined }],
+        ignoreUndefinedInKeys: true,
+      })
+      expect(queryFnAll).toHaveBeenCalledTimes(3)
+      expect(queryFnFiltered).toHaveBeenCalledTimes(2)
+
+      u1()
+      u2()
+    })
   })
 
   describe('resetQueries', () => {
diff --git a/packages/query-core/src/__tests__/utils.test.tsx b/packages/query-core/src/__tests__/utils.test.tsx
index 69c72a50aa8..1e37915d2c8 100644
--- a/packages/query-core/src/__tests__/utils.test.tsx
+++ b/packages/query-core/src/__tests__/utils.test.tsx
@@ -165,6 +165,48 @@ describe('core/utils', () => {
       const b = [{ a: null, c: 'c', d: [{ d: 'd ' }] }]
       expect(partialMatchKey(a, b)).toEqual(false)
     })
+
+    // Regression tests for https://github.com/TanStack/query/issues/3741
+    describe('with ignoreUndefinedInKeys option', () => {
+      it('should match when b has `undefined` for a key that holds a concrete value in a — only when option is enabled', () => {
+        const a = [{ entity: 'todos', filter: { done: true } }]
+        const b = [{ entity: 'todos', filter: undefined }]
+        // Default behavior: typeof mismatch between {done:true} and undefined → no match
+        expect(partialMatchKey(a, b)).toEqual(false)
+        // Opt-in: undefined in b is ignored → falls back to entity-only match
+        expect(partialMatchKey(a, b, { ignoreUndefinedInKeys: true })).toEqual(
+          true,
+        )
+      })
+
+      it('should still not match when both sides have concrete but different values', () => {
+        const a = [{ entity: 'todos', filter: { done: true } }]
+        const b = [{ entity: 'todos', filter: { done: false } }]
+        expect(partialMatchKey(a, b, { ignoreUndefinedInKeys: true })).toEqual(
+          false,
+        )
+      })
+
+      it('should not strip undefined from arrays inside the key', () => {
+        const a = [{ entity: 'todos', tags: ['urgent'] }]
+        const b = [{ entity: 'todos', tags: [undefined] }]
+        expect(partialMatchKey(a, b, { ignoreUndefinedInKeys: true })).toEqual(
+          false,
+        )
+      })
+
+      it('should match recursively in nested objects', () => {
+        const a = [{ entity: 'todos', filter: { done: true, owner: 'me' } }]
+        const b = [
+          { entity: 'todos', filter: { done: true, owner: undefined } },
+        ]
+        // Default: owner undefined vs 'me' → typeof mismatch → false
+        expect(partialMatchKey(a, b)).toEqual(false)
+        expect(partialMatchKey(a, b, { ignoreUndefinedInKeys: true })).toEqual(
+          true,
+        )
+      })
+    })
   })
 
   describe('replaceEqualDeep', () => {
diff --git a/packages/query-core/src/index.ts b/packages/query-core/src/index.ts
index a4267aabc97..4163a766633 100644
--- a/packages/query-core/src/index.ts
+++ b/packages/query-core/src/index.ts
@@ -38,7 +38,13 @@ export {
   shouldThrowError,
   skipToken,
 } from './utils'
-export type { MutationFilters, QueryFilters, SkipToken, Updater } from './utils'
+export type {
+  MutationFilters,
+  PartialMatchKeyOptions,
+  QueryFilters,
+  SkipToken,
+  Updater,
+} from './utils'
 
 export { streamedQuery as experimental_streamedQuery } from './streamedQuery'
 
diff --git a/packages/query-core/src/utils.ts b/packages/query-core/src/utils.ts
index b97b2cc5a33..8df3241d199 100644
--- a/packages/query-core/src/utils.ts
+++ b/packages/query-core/src/utils.ts
@@ -52,6 +52,15 @@ export interface QueryFilters<TQueryKey extends QueryKey = QueryKey> {
    * Include queries matching their fetchStatus
    */
   fetchStatus?: FetchStatus
+  /**
+   * When `true`, object properties whose value is `undefined` are ignored
+   * during partial query key matching. Mirrors the default `hashKey`
+   * behavior which already strips `undefined` via `JSON.stringify`.
+   *
+   * @default false
+   * @see https://github.com/TanStack/query/issues/3741
+   */
+  ignoreUndefinedInKeys?: boolean
 }
 
 export interface MutationFilters<
@@ -78,6 +87,14 @@ export interface MutationFilters<
    * Filter by mutation status
    */
   status?: MutationStatus
+  /**
+   * When `true`, object properties whose value is `undefined` are ignored
+   * during partial mutation key matching.
+   *
+   * @default false
+   * @see https://github.com/TanStack/query/issues/3741
+   */
+  ignoreUndefinedInKeys?: boolean
 }
 
 export type Updater<TInput, TOutput> = TOutput | ((input: TInput) => TOutput)
@@ -148,6 +165,7 @@ export function matchQuery(
     type = 'all',
     exact,
     fetchStatus,
+    ignoreUndefinedInKeys,
     predicate,
     queryKey,
     stale,
@@ -158,7 +176,9 @@ export function matchQuery(
       if (query.queryHash !== hashQueryKeyByOptions(queryKey, query.options)) {
         return false
       }
-    } else if (!partialMatchKey(query.queryKey, queryKey)) {
+    } else if (
+      !partialMatchKey(query.queryKey, queryKey, { ignoreUndefinedInKeys })
+    ) {
       return false
     }
   }
@@ -192,7 +212,8 @@ export function matchMutation(
   filters: MutationFilters,
   mutation: Mutation<any, any>,
 ): boolean {
-  const { exact, status, predicate, mutationKey } = filters
+  const { exact, ignoreUndefinedInKeys, status, predicate, mutationKey } =
+    filters
   if (mutationKey) {
     if (!mutation.options.mutationKey) {
       return false
@@ -201,7 +222,11 @@ export function matchMutation(
       if (hashKey(mutation.options.mutationKey) !== hashKey(mutationKey)) {
         return false
       }
-    } else if (!partialMatchKey(mutation.options.mutationKey, mutationKey)) {
+    } else if (
+      !partialMatchKey(mutation.options.mutationKey, mutationKey, {
+        ignoreUndefinedInKeys,
+      })
+    ) {
       return false
     }
   }
@@ -242,11 +267,33 @@ export function hashKey(queryKey: QueryKey | MutationKey): string {
   )
 }
 
+export type PartialMatchKeyOptions = {
+  /**
+   * When `true`, object properties whose value is `undefined` are treated as
+   * missing in both keys before comparison. This matches the behavior of the
+   * default `hashKey` (which strips `undefined` via `JSON.stringify`).
+   *
+   * Does NOT apply to `undefined` values inside arrays.
+   *
+   * @default false
+   * @see https://github.com/TanStack/query/issues/3741
+   */
+  ignoreUndefinedInKeys?: boolean
+}
+
 /**
  * Checks if key `b` partially matches with key `a`.
  */
-export function partialMatchKey(a: QueryKey, b: QueryKey): boolean
-export function partialMatchKey(a: any, b: any): boolean {
+export function partialMatchKey(
+  a: QueryKey,
+  b: QueryKey,
+  options?: PartialMatchKeyOptions,
+): boolean
+export function partialMatchKey(
+  a: any,
+  b: any,
+  options?: PartialMatchKeyOptions,
+): boolean {
   if (a === b) {
     return true
   }
@@ -256,7 +303,19 @@ export function partialMatchKey(a: any, b: any): boolean {
   }
 
   if (a && b && typeof a === 'object' && typeof b === 'object') {
-    return Object.keys(b).every((key) => partialMatchKey(a[key], b[key]))
+    if (
+      options?.ignoreUndefinedInKeys &&
+      isPlainObject(a) &&
+      isPlainObject(b)
+    ) {
+      return Object.keys(b)
+        .filter((key) => b[key] !== undefined)
+        .every((key) => partialMatchKey(a[key] as any, b[key] as any, options))
+    }
+
+    return Object.keys(b).every((key) =>
+      partialMatchKey(a[key], b[key], options),
+    )
   }
 
   return false