diff --git a/packages/plugins/agent-codex/src/app-server-client.test.ts b/packages/plugins/agent-codex/src/app-server-client.test.ts
index 1e58489c0..47eb7e991 100644
--- a/packages/plugins/agent-codex/src/app-server-client.test.ts
+++ b/packages/plugins/agent-codex/src/app-server-client.test.ts
@@ -137,8 +137,10 @@ describe("CodexAppServerClient", () => {
       // Should have sent initialize request and initialized notification
       const initReq = findRequest(proc, "initialize");
       expect(initReq).toBeDefined();
+      expect(initReq!["jsonrpc"]).toBe("2.0");
       const initializedNotif = findRequest(proc, "initialized");
       expect(initializedNotif).toBeDefined();
+      expect(initializedNotif!["jsonrpc"]).toBe("2.0");
 
       await closeClient(client, proc);
     });
diff --git a/packages/plugins/agent-codex/src/app-server-client.ts b/packages/plugins/agent-codex/src/app-server-client.ts
index 74bd5f4ce..5d5a753c2 100644
--- a/packages/plugins/agent-codex/src/app-server-client.ts
+++ b/packages/plugins/agent-codex/src/app-server-client.ts
@@ -19,6 +19,7 @@ import { EventEmitter } from "node:events";
 
 /** JSON-RPC request sent from client to server */
 export interface JsonRpcRequest {
+  jsonrpc: "2.0";
   id: string;
   method: string;
   params: Record<string, unknown>;
@@ -339,7 +340,7 @@ export class CodexAppServerClient extends EventEmitter {
     }
 
     const id = randomUUID();
-    const request: JsonRpcRequest = { id, method, params };
+    const request: JsonRpcRequest = { jsonrpc: "2.0", id, method, params };
 
     return new Promise<Record<string, unknown>>((resolve, reject) => {
       const timer = setTimeout(() => {
@@ -357,7 +358,7 @@ export class CodexAppServerClient extends EventEmitter {
     if (this.closed) return;
     if (!this.process?.stdin?.writable) return;
 
-    this.writeLine(JSON.stringify({ method, params }));
+    this.writeLine(JSON.stringify({ jsonrpc: "2.0", method, params }));
   }
 
   /** Respond to an approval request from the server */
@@ -365,7 +366,7 @@ export class CodexAppServerClient extends EventEmitter {
     if (this.closed) return;
     if (!this.process?.stdin?.writable) return;
 
-    this.writeLine(JSON.stringify({ id, result: { decision } }));
+    this.writeLine(JSON.stringify({ jsonrpc: "2.0", id, result: { decision } }));
   }
 
   // ---------------------------------------------------------------------------
diff --git a/packages/plugins/agent-codex/src/index.test.ts b/packages/plugins/agent-codex/src/index.test.ts
index 9bf4d11fd..5ddbc5057 100644
--- a/packages/plugins/agent-codex/src/index.test.ts
+++ b/packages/plugins/agent-codex/src/index.test.ts
@@ -942,6 +942,30 @@ describe("getRestoreCommand", () => {
     expect(cmd).toContain("--ask-for-approval untrusted");
   });
 
+  it("places flags before positional threadId in resume command", async () => {
+    const content = jsonl(
+      { type: "session_meta", cwd: "/workspace/test", model: "o3-mini" },
+      { threadId: "thread-order-test" },
+    );
+    mockReaddir.mockResolvedValue(["sess.jsonl"]);
+    setupMockOpen(content);
+    mockReadFile.mockResolvedValue(content);
+    mockStat.mockResolvedValue({ mtimeMs: 1000 });
+
+    const session = makeSession({ workspacePath: "/workspace/test" });
+    const cmd = await agent.getRestoreCommand!(session, makeProjectConfig({
+      agentConfig: { permissions: "auto-edit", model: "o3-mini" },
+    }));
+
+    expect(cmd).not.toBeNull();
+    // threadId should come after all flags
+    const threadIdIdx = cmd!.indexOf("thread-order-test");
+    const flagIdx = cmd!.indexOf("--ask-for-approval");
+    const modelIdx = cmd!.indexOf("--model");
+    expect(flagIdx).toBeLessThan(threadIdIdx);
+    expect(modelIdx).toBeLessThan(threadIdIdx);
+  });
+
   it("includes model from project config (overrides session model)", async () => {
     const content = jsonl(
       { type: "session_meta", cwd: "/workspace/test", model: "gpt-4o" },
diff --git a/packages/plugins/agent-codex/src/index.ts b/packages/plugins/agent-codex/src/index.ts
index ced06398b..25a9c681a 100644
--- a/packages/plugins/agent-codex/src/index.ts
+++ b/packages/plugins/agent-codex/src/index.ts
@@ -732,8 +732,9 @@ function createCodexAgent(): Agent {
 
       // Use Codex's native `resume` subcommand for proper conversation resume.
       // This restores the full thread state, not just a text prompt re-injection.
+      // Flags are placed before the positional threadId for CLI parser compatibility.
       const binary = resolvedBinary ?? "codex";
-      const parts: string[] = [binary, "resume", shellEscape(threadId)];
+      const parts: string[] = [binary, "resume"];
 
       // Add approval policy flags from project config
       const perms = project.agentConfig?.permissions as string | undefined;
@@ -754,6 +755,9 @@ function createCodexAgent(): Agent {
         }
       }
 
+      // Positional threadId goes last, after all flags
+      parts.push(shellEscape(threadId));
+
       return parts.join(" ");
     },