diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 3bb5b85e..f2404bb0 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -84,6 +84,8 @@ export class MCPServerConfig {
     readonly trust?: boolean,
     // Metadata
     readonly description?: string,
+    readonly includeTools?: string[],
+    readonly excludeTools?: string[],
   ) {}
 }
 
diff --git a/packages/core/src/tools/mcp-client.test.ts b/packages/core/src/tools/mcp-client.test.ts
index 09f7951b..1413a4f8 100644
--- a/packages/core/src/tools/mcp-client.test.ts
+++ b/packages/core/src/tools/mcp-client.test.ts
@@ -668,6 +668,115 @@ describe('discoverMcpTools', () => {
       clientInstances[clientInstances.length - 1]?.value;
     expect(lastClientInstance?.onerror).toEqual(expect.any(Function));
   });
+
+  describe('Tool Filtering', () => {
+    const mockTools = [
+      {
+        name: 'toolA',
+        description: 'descA',
+        inputSchema: { type: 'object' as const, properties: {} },
+      },
+      {
+        name: 'toolB',
+        description: 'descB',
+        inputSchema: { type: 'object' as const, properties: {} },
+      },
+      {
+        name: 'toolC',
+        description: 'descC',
+        inputSchema: { type: 'object' as const, properties: {} },
+      },
+    ];
+
+    beforeEach(() => {
+      vi.mocked(Client.prototype.listTools).mockResolvedValue({
+        tools: mockTools,
+      });
+      mockToolRegistry.getToolsByServer.mockReturnValue([
+        expect.any(DiscoveredMCPTool),
+      ]);
+    });
+
+    it('should only include specified tools with includeTools', async () => {
+      const serverConfig: MCPServerConfig = {
+        command: './mcp-include',
+        includeTools: ['toolA', 'toolC'],
+      };
+      mockConfig.getMcpServers.mockReturnValue({
+        'include-server': serverConfig,
+      });
+
+      await discoverMcpTools(
+        mockConfig.getMcpServers() ?? {},
+        mockConfig.getMcpServerCommand(),
+        mockToolRegistry as any,
+      );
+
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledTimes(2);
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolA' }),
+      );
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolC' }),
+      );
+      expect(mockToolRegistry.registerTool).not.toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolB' }),
+      );
+    });
+
+    it('should exclude specified tools with excludeTools', async () => {
+      const serverConfig: MCPServerConfig = {
+        command: './mcp-exclude',
+        excludeTools: ['toolB'],
+      };
+      mockConfig.getMcpServers.mockReturnValue({
+        'exclude-server': serverConfig,
+      });
+
+      await discoverMcpTools(
+        mockConfig.getMcpServers() ?? {},
+        mockConfig.getMcpServerCommand(),
+        mockToolRegistry as any,
+      );
+
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledTimes(2);
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolA' }),
+      );
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolC' }),
+      );
+      expect(mockToolRegistry.registerTool).not.toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolB' }),
+      );
+    });
+
+    it('should handle both includeTools and excludeTools', async () => {
+      const serverConfig: MCPServerConfig = {
+        command: './mcp-both',
+        includeTools: ['toolA', 'toolB'],
+        excludeTools: ['toolB'],
+      };
+      mockConfig.getMcpServers.mockReturnValue({ 'both-server': serverConfig });
+
+      await discoverMcpTools(
+        mockConfig.getMcpServers() ?? {},
+        mockConfig.getMcpServerCommand(),
+        mockToolRegistry as any,
+      );
+
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledTimes(1);
+      expect(mockToolRegistry.registerTool).toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolA' }),
+      );
+      expect(mockToolRegistry.registerTool).not.toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolB' }),
+      );
+      expect(mockToolRegistry.registerTool).not.toHaveBeenCalledWith(
+        expect.objectContaining({ serverToolName: 'toolC' }),
+      );
+    });
+  });
 });
 
 describe('sanitizeParameters', () => {
diff --git a/packages/core/src/tools/mcp-client.ts b/packages/core/src/tools/mcp-client.ts
index bb92ab05..6dca8cea 100644
--- a/packages/core/src/tools/mcp-client.ts
+++ b/packages/core/src/tools/mcp-client.ts
@@ -305,6 +305,26 @@ async function connectAndDiscover(
         continue;
       }
 
+      const { includeTools, excludeTools } = mcpServerConfig;
+      const toolName = funcDecl.name;
+
+      let isEnabled = false;
+      if (includeTools === undefined) {
+        isEnabled = true;
+      } else {
+        isEnabled = includeTools.some(
+          (tool) => tool === toolName || tool.startsWith(`${toolName}(`),
+        );
+      }
+
+      if (excludeTools?.includes(toolName)) {
+        isEnabled = false;
+      }
+
+      if (!isEnabled) {
+        continue;
+      }
+
       let toolNameForModel = funcDecl.name;
 
       // Replace invalid characters (based on 400 error message from Gemini API) with underscores