diff --git a/.changeset/fix-jsonrpc-error-nonexistent-tool.md b/.changeset/fix-jsonrpc-error-nonexistent-tool.md
new file mode 100644
index 000000000..46020cb1e
--- /dev/null
+++ b/.changeset/fix-jsonrpc-error-nonexistent-tool.md
@@ -0,0 +1,7 @@
+---
+"@modelcontextprotocol/sdk": patch
+---
+
+fix: return JSON-RPC error for nonexistent tool calls
+
+When `callTool` is invoked with a tool name that doesn't exist in the registered handlers, the server now returns a proper JSON-RPC error with code -32601 (Method not found) instead of returning an error in the content array. This aligns with JSON-RPC 2.0 specification and provides clearer error handling for clients.
diff --git a/packages/server/src/server/mcp.ts b/packages/server/src/server/mcp.ts
index 27b308285..6ca589a96 100644
--- a/packages/server/src/server/mcp.ts
+++ b/packages/server/src/server/mcp.ts
@@ -198,9 +198,20 @@ export class McpServer {
                 await this.validateToolOutput(tool, result, request.params.name);
                 return result;
             } catch (error) {
+                // Per MCP spec, tool not found should return a JSON-RPC error, not isError result
+                // https://modelcontextprotocol.io/specification/2025-11-25/server/tools#error-handling
+                if (
+                    error instanceof ProtocolError &&
+                    (error.code === ProtocolErrorCode.InvalidParams || error.code === ProtocolErrorCode.MethodNotFound) &&
+                    error.message.includes('not found')
+                ) {
+                    throw error;
+                }
+                // URL elicitation errors should propagate
                 if (error instanceof ProtocolError && error.code === ProtocolErrorCode.UrlElicitationRequired) {
-                    throw error; // Return the error to the caller without wrapping in CallToolResult
+                    throw error;
                 }
+                // Other errors (execution, validation) get wrapped in CallToolResult with isError: true
                 return this.createToolError(error instanceof Error ? error.message : String(error));
             }
         });
diff --git a/test/integration/test/server/mcp.test.ts b/test/integration/test/server/mcp.test.ts
index 091e4ac21..566cde805 100644
--- a/test/integration/test/server/mcp.test.ts
+++ b/test/integration/test/server/mcp.test.ts
@@ -1812,6 +1812,7 @@ describe('Zod v4', () => {
 
         /***
          * Test: ProtocolError for Invalid Tool Name
+         * Per MCP spec, calling a nonexistent tool should return a JSON-RPC error, not a result with isError
          */
         test('should throw ProtocolError for invalid tool name', async () => {
             const mcpServer = new McpServer({
@@ -1837,25 +1838,17 @@ describe('Zod v4', () => {
 
             await Promise.all([client.connect(clientTransport), mcpServer.server.connect(serverTransport)]);
 
-            const result = await client.request(
-                {
-                    method: 'tools/call',
-                    params: {
-                        name: 'nonexistent-tool'
-                    }
-                },
-                CallToolResultSchema
-            );
-
-            expect(result.isError).toBe(true);
-            expect(result.content).toEqual(
-                expect.arrayContaining([
+            await expect(
+                client.request(
                     {
-                        type: 'text',
-                        text: expect.stringContaining('Tool nonexistent-tool not found')
-                    }
-                ])
-            );
+                        method: 'tools/call',
+                        params: {
+                            name: 'nonexistent-tool'
+                        }
+                    },
+                    CallToolResultSchema
+                )
+            ).rejects.toThrow(/Tool nonexistent-tool not found/);
         });
 
         /***