diff --git a/.changeset/rename-then-remove.md b/.changeset/rename-then-remove.md
new file mode 100644
index 0000000000..02d11ff581
--- /dev/null
+++ b/.changeset/rename-then-remove.md
@@ -0,0 +1,13 @@
+---
+'@modelcontextprotocol/server': patch
+---
+
+Fix `remove()` being a silent no-op after a resource, resource template, or prompt
+has been renamed via `update()`. The closures for these three registration types
+captured the original registry key and never reassigned it after a rename, so
+`remove()` deleted the stale key instead of the one the entry now lives under —
+leaving the entry listed and callable, with a `list_changed` notification firing
+regardless. `RegisteredTool` already tracked its current key correctly; resources,
+resource templates, and prompts now do the same.
+
+Fixes #2723
diff --git a/packages/server/src/server/mcp.ts b/packages/server/src/server/mcp.ts
index d2e40181e4..b80c1d5f7f 100644
--- a/packages/server/src/server/mcp.ts
+++ b/packages/server/src/server/mcp.ts
@@ -675,7 +675,10 @@ export class McpServer {
             update: updates => {
                 if (updates.uri !== undefined && updates.uri !== uri) {
                     delete this._registeredResources[uri];
-                    if (updates.uri) this._registeredResources[updates.uri] = registeredResource;
+                    if (updates.uri) {
+                        this._registeredResources[updates.uri] = registeredResource;
+                        uri = updates.uri; // track the current registry key
+                    }
                 }
                 if (updates.name !== undefined) registeredResource.name = updates.name;
                 if (updates.title !== undefined) registeredResource.title = updates.title;
@@ -708,7 +711,10 @@ export class McpServer {
             update: updates => {
                 if (updates.name !== undefined && updates.name !== name) {
                     delete this._registeredResourceTemplates[name];
-                    if (updates.name) this._registeredResourceTemplates[updates.name] = registeredResourceTemplate;
+                    if (updates.name) {
+                        this._registeredResourceTemplates[updates.name] = registeredResourceTemplate;
+                        name = updates.name; // track the current registry key
+                    }
                 }
                 if (updates.title !== undefined) registeredResourceTemplate.title = updates.title;
                 if (updates.template !== undefined) registeredResourceTemplate.resourceTemplate = updates.template;
@@ -757,7 +763,12 @@ export class McpServer {
             update: updates => {
                 if (updates.name !== undefined && updates.name !== name) {
                     delete this._registeredPrompts[name];
-                    if (updates.name) this._registeredPrompts[updates.name] = registeredPrompt;
+                    if (updates.name) {
+                        this._registeredPrompts[updates.name] = registeredPrompt;
+                        // Tracks the current registry key; also feeds createPromptHandler() below, so a
+                        // rename followed by a schema change regenerates against the new name.
+                        name = updates.name;
+                    }
                 }
                 if (updates.title !== undefined) registeredPrompt.title = updates.title;
                 if (updates.description !== undefined) registeredPrompt.description = updates.description;
diff --git a/test/integration/test/issues/test2723.remove-after-rename.test.ts b/test/integration/test/issues/test2723.remove-after-rename.test.ts
new file mode 100644
index 0000000000..ffc027f4ff
--- /dev/null
+++ b/test/integration/test/issues/test2723.remove-after-rename.test.ts
@@ -0,0 +1,72 @@
+/**
+ * Regression test for https://github.com/modelcontextprotocol/typescript-sdk/issues/2723
+ *
+ * The `update` closure for prompts, resources and resource templates captured the
+ * registration key and never reassigned it, so after a rename `remove()` deleted the
+ * vacated key and left the live entry registered and callable. `RegisteredTool`
+ * already reassigned its key; these three did not.
+ */
+import { Client } from '@modelcontextprotocol/client';
+import { InMemoryTransport } from '@modelcontextprotocol/core-internal';
+import { McpServer, ResourceTemplate } from '@modelcontextprotocol/server';
+
+describe('Issue #2723: remove() after rename is a no-op', () => {
+    test('removes a prompt after it has been renamed', async () => {
+        const server = new McpServer({ name: 'test', version: '1.0.0' });
+        const prompt = server.registerPrompt('original', { description: 'x' }, async () => ({ messages: [] }));
+        prompt.update({ name: 'renamed' });
+        prompt.remove();
+
+        const client = new Client({ name: 'client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+        await Promise.all([client.connect(clientTransport), server.connect(serverTransport)]);
+
+        const result = await client.listPrompts();
+        expect(result.prompts).toHaveLength(0);
+    });
+
+    test('removes a resource after it has been renamed', async () => {
+        const server = new McpServer({ name: 'test', version: '1.0.0' });
+        const resource = server.registerResource('test', 'test://original', {}, async () => ({ contents: [] }));
+        resource.update({ uri: 'test://renamed' });
+        resource.remove();
+
+        const client = new Client({ name: 'client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+        await Promise.all([client.connect(clientTransport), server.connect(serverTransport)]);
+
+        const result = await client.listResources();
+        expect(result.resources).toHaveLength(0);
+    });
+
+    test('removes a resource template after it has been renamed', async () => {
+        const server = new McpServer({ name: 'test', version: '1.0.0' });
+        const template = server.registerResource('original', new ResourceTemplate('test://{id}', { list: undefined }), {}, async () => ({
+            contents: []
+        }));
+        template.update({ name: 'renamed' });
+        template.remove();
+
+        const client = new Client({ name: 'client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+        await Promise.all([client.connect(clientTransport), server.connect(serverTransport)]);
+
+        const result = await client.listResourceTemplates();
+        expect(result.resourceTemplates).toHaveLength(0);
+    });
+
+    test('should remove a prompt that was renamed and renamed back', async () => {
+        const server = new McpServer({ name: 'test', version: '1.0.0' });
+        const prompt = server.registerPrompt('original', { description: 'x' }, async () => ({ messages: [] }));
+        prompt.update({ name: 'renamed' });
+        prompt.update({ name: 'original' });
+        prompt.remove();
+
+        const client = new Client({ name: 'client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+        await Promise.all([client.connect(clientTransport), server.connect(serverTransport)]);
+
+        const result = await client.listPrompts();
+        expect(result.prompts).toHaveLength(0);
+    });
+});