MCP stdio server: SyntaxError Unexpected token in deserializeMessage when using console.log

Question

When I run an MCP server built with @modelcontextprotocol/typescript-sdk over stdio and start it with npx @modelcontextprotocol/inspector node ./server.js, calling a tool throws SyntaxError: Unexpected token 'g', "get_weathe"... is not valid JSON at deserializeMessage in shared/stdio.js. The tool handler logs console.log("get_weather tool called with", city) before returning its result. Why is the plain log line being parsed as JSON?

Originally asked on GitHub: https://github.com/modelcontextprotocol/typescript-sdk/issues/244

AgentArmor team · Accepted Answer

Status: explained — a contributor identified the cause and proposed a fix, but no one in the thread reported testing it.

The error happens because the stdio transport treats stdout as the JSON-RPC message channel. A plain-text `console.log("get_weather tool called with", city)` inside the tool handler is sent to stdout and therefore reaches the client as if it were a protocol message. The client's `deserializeMessage` then calls `JSON.parse` on that line, producing `SyntaxError: Unexpected token 'g'`.

A contributor stated that, per the MCP docs on logging in MCP servers, console logging should not be sent to stdio for stdio servers, and recommended using `console.error()` instead in TypeScript. That applies to all logs in a stdio server, including the startup messages in the reporter's example (`console.log("start demo MCP server...")`), since those also go to stdout and corrupt the protocol stream.

The reporter reproduced the issue with `npx @modelcontextprotocol/inspector node ./server.js` using `McpServer` and `StdioServerTransport` from the TypeScript SDK. The reporter's suggested alternative — making `deserializeMessage` check whether the input is JSON before parsing — was not tested or adopted in the thread. Note that whether switching to `console.error()` actually resolves the error is not confirmed anywhere in the thread, so treat it as a proposed fix rather than a verified one.

AgentArmor team · Answer

**What @bhosmer-ant tried on GitHub** (Outcome unclear)

A contributor stated that for stdio servers console logging should not be sent to stdout, pointed to the MCP docs on logging in servers, and suggested using `console.error()` instead of `console.log()` in TypeScript.

Source: https://github.com/modelcontextprotocol/typescript-sdk/issues/244#issuecomment-3371981308

AgentArmor team · Answer

**What @karmiy tried on GitHub** (Outcome unclear)

Reproduced the error with the posted server code (a `get_weather` tool with a `console.log` in the handler) started via `npx @modelcontextprotocol/inspector node ./server.js`.

Source: https://github.com/modelcontextprotocol/typescript-sdk/issues/244#issuecomment-2765274361

AgentArmor team · Answer

**What @karmiy tried on GitHub** (Outcome unclear)

Reported the bug and proposed either making `deserializeMessage` check whether the incoming line is JSON before parsing, or changing the tool-call notification format to valid JSON.

Source: https://github.com/modelcontextprotocol/typescript-sdk/issues/244

MCP stdio server: SyntaxError Unexpected token in deserializeMessage when using console.log

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MCP stdio server: SyntaxError Unexpected token in deserializeMessage when using console.log

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