diff --git a/packages/coding-agent/src/mcp/transports/header-policy.ts b/packages/coding-agent/src/mcp/transports/header-policy.ts
index ee278e22e..590f71443 100644
--- a/packages/coding-agent/src/mcp/transports/header-policy.ts
+++ b/packages/coding-agent/src/mcp/transports/header-policy.ts
@@ -48,6 +48,34 @@ export function setGeneratedHeader(headers: Record<string, string>, name: string
 	headers[name] = value;
 }
 
+/**
+ * Return `headers` without any entry whose name case-insensitively matches
+ * `name`. Used to keep transport-reserved protocol headers (e.g.
+ * `MCP-Protocol-Version`) out of user-configured headers so config can never
+ * inject them. Returns the original reference when there is nothing to strip,
+ * so the common (no-match) path allocates nothing.
+ */
+export function withoutHeader(
+	headers: Record<string, string> | undefined,
+	name: string,
+): Record<string, string> | undefined {
+	if (!headers) return headers;
+	const lower = name.toLowerCase();
+	let hasMatch = false;
+	for (const key in headers) {
+		if (key.toLowerCase() === lower) {
+			hasMatch = true;
+			break;
+		}
+	}
+	if (!hasMatch) return headers;
+	const result: Record<string, string> = {};
+	for (const key in headers) {
+		if (key.toLowerCase() !== lower) result[key] = headers[key];
+	}
+	return result;
+}
+
 const REDIRECT_STATUSES: Record<number, true> = { 301: true, 302: true, 303: true, 307: true, 308: true };
 const MAX_REDIRECT_HOPS = 5;
 
diff --git a/packages/coding-agent/src/mcp/transports/http.ts b/packages/coding-agent/src/mcp/transports/http.ts
index 6a1acac12..86b22909a 100644
--- a/packages/coding-agent/src/mcp/transports/http.ts
+++ b/packages/coding-agent/src/mcp/transports/http.ts
@@ -20,7 +20,7 @@ import type {
 import { toJsonRpcError } from "../../mcp/types";
 import { RequestIdAllocator } from "../request-id";
 import { createMCPTimeout, getNeverAbortSignal, isMCPTimeoutEnabled, resolveMCPTimeoutMs } from "../timeout";
-import { type MCPFetchInit, mcpFetch } from "./header-policy";
+import { type MCPFetchInit, mcpFetch, withoutHeader } from "./header-policy";
 
 const HTTP_SSE_CONNECT_TIMEOUT_MS = 1_000;
 /**
@@ -67,18 +67,20 @@ export class HttpTransport implements MCPTransport {
 	/**
 	 * Fetch the configured endpoint with header precedence and origin policy.
 	 *
-	 * Once a version is negotiated, every request carries `MCP-Protocol-Version`
-	 * (required by the MCP Streamable HTTP spec after `initialize`). It rides
-	 * under `generated` so it wins over a same-named configured header. Before
-	 * negotiation (the `initialize` request itself) the header is omitted.
+	 * The transport fully owns `MCP-Protocol-Version`: it is stripped from
+	 * configured headers so a user's `mcp.json` can never inject it, and added
+	 * only once a version is negotiated (required by the MCP Streamable HTTP spec
+	 * after `initialize`). Before negotiation — the `initialize` request itself —
+	 * no protocol-version header is sent from either source.
 	 */
 	#fetch(init: MCPFetchInit, generated: Record<string, string>): Promise<Response> {
+		const configured = withoutHeader(this.config.headers, "MCP-Protocol-Version");
 		const withVersion =
 			this.#protocolVersion === null ? generated : { "MCP-Protocol-Version": this.#protocolVersion, ...generated };
 		return mcpFetch(
 			this.config.url,
 			init,
-			{ generated: withVersion, configured: this.config.headers },
+			{ generated: withVersion, configured },
 			this.config.headerPolicy === "origin-locked",
 		);
 	}
diff --git a/packages/coding-agent/test/mcp-http-transport.test.ts b/packages/coding-agent/test/mcp-http-transport.test.ts
index 812fe4a7d..e1f2244df 100644
--- a/packages/coding-agent/test/mcp-http-transport.test.ts
+++ b/packages/coding-agent/test/mcp-http-transport.test.ts
@@ -137,4 +137,36 @@ describe("MCP Streamable HTTP protocol version header", () => {
 		await withPendingGuard(transport.request("tools/list"), "request");
 		expect(seen.version).toBe("2025-06-18");
 	});
+
+	it("never lets a configured MCP-Protocol-Version reach the server", async () => {
+		const seen: { pre: string | null; post: string | null } = { pre: null, post: null };
+		server = Bun.serve({
+			port: 0,
+			fetch(req) {
+				const body = req.headers.get("MCP-Protocol-Version");
+				return Response.json({ jsonrpc: "2.0", id: 1, result: { seen: body } });
+			},
+		});
+		if (!server) throw new Error("Test server was not started");
+		const transport = new HttpTransport({
+			type: "http",
+			url: `http://127.0.0.1:${server.port}/mcp`,
+			timeout: REQUEST_TIMEOUT_MS,
+			headers: { "MCP-Protocol-Version": "1999-01-01" },
+		});
+		await transport.connect();
+
+		// Pre-negotiation: configured header must be stripped, not leaked.
+		seen.pre = await withPendingGuard(transport.request<{ seen: string | null }>("initialize"), "request").then(
+			r => r.seen,
+		);
+		// Post-negotiation: the negotiated version wins over the configured one.
+		transport.setProtocolVersion("2025-11-25");
+		seen.post = await withPendingGuard(transport.request<{ seen: string | null }>("tools/list"), "request").then(
+			r => r.seen,
+		);
+
+		expect(seen.pre).toBeNull();
+		expect(seen.post).toBe("2025-11-25");
+	});
 });