diff --git a/CLAUDE.md b/CLAUDE.md
index 6e768e559..2cbb850df 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -22,7 +22,7 @@ npm run typecheck    # Type-check without emitting
 - **Files**: Lowercase with hyphens, test files with `.test.ts` suffix
 - **Imports**: ES module style, include `.js` extension, group imports logically
 - **Formatting**: 2-space indentation, semicolons required, single quotes preferred
-- **Testing**: Co-locate tests with source files, use descriptive test names
+- **Testing**: Co-locate tests with source files, use descriptive test names. Use `vi.useFakeTimers()` instead of real `setTimeout`/`await` delays in tests
 - **Comments**: JSDoc for public APIs, inline comments for complex logic
 
 ## Architecture Overview
diff --git a/src/shared/protocol.ts b/src/shared/protocol.ts
index aa242a647..7bc7714d7 100644
--- a/src/shared/protocol.ts
+++ b/src/shared/protocol.ts
@@ -642,6 +642,11 @@ export abstract class Protocol<SendRequestT extends Request, SendNotificationT e
         this._taskProgressTokens.clear();
         this._pendingDebouncedNotifications.clear();
 
+        for (const info of this._timeoutInfo.values()) {
+            clearTimeout(info.timeoutId);
+        }
+        this._timeoutInfo.clear();
+
         const error = McpError.fromError(ErrorCode.ConnectionClosed, 'Connection closed');
 
         this._transport = undefined;
@@ -824,7 +829,11 @@ export abstract class Protocol<SendRequestT extends Request, SendNotificationT e
             )
             .catch(error => this._onerror(new Error(`Failed to send response: ${error}`)))
             .finally(() => {
-                this._requestHandlerAbortControllers.delete(request.id);
+                // Only delete if the stored controller is still ours; after close()+connect(),
+                // a new connection may have reused the same request ID with a different controller.
+                if (this._requestHandlerAbortControllers.get(request.id) === abortController) {
+                    this._requestHandlerAbortControllers.delete(request.id);
+                }
             });
     }
 
diff --git a/test/shared/protocol.test.ts b/test/shared/protocol.test.ts
index 886dcbb21..733146f29 100644
--- a/test/shared/protocol.test.ts
+++ b/test/shared/protocol.test.ts
@@ -5556,3 +5556,162 @@ describe('Error handling for missing resolvers', () => {
         });
     });
 });
+
+describe('_onclose cleanup', () => {
+    let protocol: Protocol<Request, Notification, Result>;
+    let transport: MockTransport;
+    let sendSpy: MockInstance;
+
+    beforeEach(() => {
+        vi.useFakeTimers();
+        transport = new MockTransport();
+        sendSpy = vi.spyOn(transport, 'send');
+        protocol = new (class extends Protocol<Request, Notification, Result> {
+            protected assertCapabilityForMethod(): void {}
+            protected assertNotificationCapability(): void {}
+            protected assertRequestHandlerCapability(): void {}
+            protected assertTaskCapability(): void {}
+            protected assertTaskHandlerCapability(): void {}
+        })();
+    });
+
+    afterEach(() => {
+        vi.useRealTimers();
+    });
+
+    test('should clear pending timeouts in _onclose to prevent spurious cancellation after reconnect', async () => {
+        await protocol.connect(transport);
+
+        // Start a request with a long timeout
+        const request = { method: 'example', params: {} };
+        const mockSchema = z.object({ result: z.string() });
+
+        const requestPromise = protocol
+            .request(request, mockSchema, {
+                timeout: 60000
+            })
+            .catch(() => {
+                /* expected ConnectionClosed error */
+            });
+
+        // Verify the request was sent
+        expect(sendSpy).toHaveBeenCalled();
+
+        // Spy on clearTimeout to verify it gets called during close
+        const clearTimeoutSpy = vi.spyOn(global, 'clearTimeout');
+
+        // Close the transport - this should clear timeouts
+        await transport.close();
+
+        // Verify clearTimeout was called (at least once for our timeout)
+        expect(clearTimeoutSpy).toHaveBeenCalled();
+
+        // Now reconnect with a new transport
+        const transport2 = new MockTransport();
+        const sendSpy2 = vi.spyOn(transport2, 'send');
+        await protocol.connect(transport2);
+
+        // Advance past the original timeout - if not cleared, this would fire the callback
+        await vi.advanceTimersByTimeAsync(60000);
+
+        // Verify no spurious cancellation notification was sent to the new transport
+        const cancellationCalls = sendSpy2.mock.calls.filter(call => {
+            const msg = call[0] as Record<string, unknown>;
+            return msg.method === 'notifications/cancelled';
+        });
+        expect(cancellationCalls).toHaveLength(0);
+
+        await transport2.close();
+        await requestPromise;
+        clearTimeoutSpy.mockRestore();
+    });
+
+    test('should not let stale .finally() delete a new connections abort controller after reconnect', async () => {
+        await protocol.connect(transport);
+
+        const TestRequestSchema = z.object({
+            method: z.literal('test/longRunning'),
+            params: z.optional(z.record(z.unknown()))
+        });
+
+        // Set up a handler with a deferred resolution we control
+        let resolveHandler!: () => void;
+        const handlerStarted = new Promise<void>(resolve => {
+            protocol.setRequestHandler(TestRequestSchema, async () => {
+                resolve(); // signal that handler has started
+                // Wait for explicit resolution
+                await new Promise<void>(r => {
+                    resolveHandler = r;
+                });
+                return { _meta: {} } as Result;
+            });
+        });
+
+        // Simulate an incoming request with id=1 on the first connection
+        const requestId = 1;
+        transport.onmessage!({
+            jsonrpc: '2.0',
+            id: requestId,
+            method: 'test/longRunning',
+            params: {}
+        });
+
+        // Wait for handler to start
+        await handlerStarted;
+
+        // Close the connection (aborts the controller and clears the map)
+        await transport.close();
+
+        // Reconnect with a new transport
+        const transport2 = new MockTransport();
+        await protocol.connect(transport2);
+
+        // Set up a new handler for the second connection that we can verify cancellation on
+        let wasAborted = false;
+        let resolveHandler2!: () => void;
+        const handler2Started = new Promise<void>(resolve => {
+            protocol.setRequestHandler(TestRequestSchema, async (_request, extra) => {
+                resolve();
+                await new Promise<void>(r => {
+                    resolveHandler2 = r;
+                });
+                wasAborted = extra.signal.aborted;
+                return { _meta: {} } as Result;
+            });
+        });
+
+        // Simulate same request id=1 on the new connection
+        transport2.onmessage!({
+            jsonrpc: '2.0',
+            id: requestId,
+            method: 'test/longRunning',
+            params: {}
+        });
+
+        await handler2Started;
+
+        // Resolve the OLD handler so its .finally() runs
+        resolveHandler();
+        // Flush microtasks so .finally() executes
+        await vi.advanceTimersByTimeAsync(0);
+
+        // Send cancellation for request id=1 on the new connection.
+        // If the old .finally() incorrectly deleted the new controller, this won't work.
+        transport2.onmessage!({
+            jsonrpc: '2.0',
+            method: 'notifications/cancelled',
+            params: {
+                requestId: requestId,
+                reason: 'test cancel'
+            }
+        });
+
+        // Resolve handler2 so it can check the abort signal
+        resolveHandler2();
+        await vi.advanceTimersByTimeAsync(0);
+
+        expect(wasAborted).toBe(true);
+
+        await transport2.close();
+    });
+});