diff --git a/docs/testcases.md b/docs/testcases.md
index d829e6b..d7a57d2 100644
--- a/docs/testcases.md
+++ b/docs/testcases.md
@@ -197,6 +197,13 @@ Run explicitly with `bun run test:e2e` (not included in `bun test`).
 - CLI invoked via `Bun.spawn` running `bun run src/index.ts <command> --yes`
 - On test failure, state file is kept and a manual cleanup message is displayed
 
+### CLI Prompt Handling
+
+| # | Case | Input | Expected |
+|---|------|-------|----------|
+| C-1 | Apply confirmation accepts affirmative answers | `y`, `yes`, mixed case, surrounding whitespace | Apply continues |
+| C-2 | Apply confirmation defaults to no | empty input, `n`, `no` | Apply is cancelled |
+
 ### E2E-1: Full Lifecycle
 
 Precondition: agup.yaml with environment + skill + agent placed in temp directory
diff --git a/packages/cli/src/index.test.ts b/packages/cli/src/index.test.ts
index 03bd35b..c915815 100644
--- a/packages/cli/src/index.test.ts
+++ b/packages/cli/src/index.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, test } from "bun:test";
-import { parseCliArgs } from "./index.ts";
+import { parseCliArgs, parseConfirmationAnswer } from "./index.ts";
 
 describe("parseCliArgs", () => {
   test("parses global options before the command", () => {
@@ -78,3 +78,17 @@ describe("parseCliArgs", () => {
     );
   });
 });
+
+describe("parseConfirmationAnswer", () => {
+  test("accepts y and yes in a case-insensitive way", () => {
+    expect(parseConfirmationAnswer("y")).toBe(true);
+    expect(parseConfirmationAnswer("YES")).toBe(true);
+    expect(parseConfirmationAnswer(" yes ")).toBe(true);
+  });
+
+  test("rejects empty and non-affirmative answers", () => {
+    expect(parseConfirmationAnswer("")).toBe(false);
+    expect(parseConfirmationAnswer("n")).toBe(false);
+    expect(parseConfirmationAnswer("no")).toBe(false);
+  });
+});
diff --git a/packages/cli/src/index.ts b/packages/cli/src/index.ts
index 593d054..93d703a 100644
--- a/packages/cli/src/index.ts
+++ b/packages/cli/src/index.ts
@@ -1,5 +1,6 @@
 import * as fs from "node:fs/promises";
 import * as path from "node:path";
+import { createInterface } from "node:readline/promises";
 import { fileURLToPath } from "node:url";
 import {
   parseYaml,
@@ -304,13 +305,23 @@ function operationDetail(op: Operation): string {
   }
 }
 
+export function parseConfirmationAnswer(answer: string): boolean {
+  const normalized = answer.trim().toLowerCase();
+  return normalized === "y" || normalized === "yes";
+}
+
 async function confirm(message: string): Promise<boolean> {
-  process.stdout.write(`${message} [y/N] `);
-  for await (const line of console) {
-    const answer = (line as string).trim().toLowerCase();
-    return answer === "y" || answer === "yes";
+  const rl = createInterface({
+    input: process.stdin,
+    output: process.stdout,
+  });
+
+  try {
+    const answer = await rl.question(`${message} [y/N] `);
+    return parseConfirmationAnswer(answer);
+  } finally {
+    rl.close();
   }
-  return false;
 }
 
 async function createApiClient(): Promise<ApiClient> {