diff --git a/cli/tests/integration/run_tests.rs b/cli/tests/integration/run_tests.rs
index c91169f1a6..564b7355fc 100644
--- a/cli/tests/integration/run_tests.rs
+++ b/cli/tests/integration/run_tests.rs
@@ -3723,3 +3723,23 @@ fn file_fetcher_preserves_permissions() {
     assert_contains!(output, "true");
   });
 }
+
+#[test]
+fn stdio_streams_are_locked_in_permission_prompt() {
+  let _guard = util::http_server();
+  util::with_pty(&[
+    "repl",
+    "--allow-read=run/stdio_streams_are_locked_in_permission_prompt/worker.js,run/stdio_streams_are_locked_in_permission_prompt/text.txt"
+    ], |mut console| {
+    console.write_line(
+      r#"new Worker(`${Deno.cwd()}/run/stdio_streams_are_locked_in_permissions_prompt/worker.js`, { type: "module" });
+      await Deno.writeTextFile("./run/stdio_streams_are_locked_in_permissions_prompt/text.txt", "some code");"#,
+    );
+    console.write_line("y");
+    console.write_line("close();");
+    let output = console.read_all_output();
+
+    let expected_output = r#"\x1b[1;1H\x1b[0JAre you sure you want to continue?"#;
+    assert_eq!(output, expected_output);
+  });
+}
diff --git a/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/text.txt b/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/text.txt
new file mode 100644
index 0000000000..e6177e9cf8
--- /dev/null
+++ b/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/text.txt
@@ -0,0 +1 @@
+\x1B[2J\x1B[1;1H
\ No newline at end of file
diff --git a/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/worker.js b/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/worker.js
new file mode 100644
index 0000000000..6d67c51a2a
--- /dev/null
+++ b/cli/tests/testdata/run/stdio_streams_are_locked_in_permission_prompt/worker.js
@@ -0,0 +1,2 @@
+console.clear();
+console.log("Are you sure you want to continue?");
diff --git a/runtime/permissions/prompter.rs b/runtime/permissions/prompter.rs
index a738988355..ae07e004c8 100644
--- a/runtime/permissions/prompter.rs
+++ b/runtime/permissions/prompter.rs
@@ -192,6 +192,11 @@ impl PermissionPrompter for TtyPrompter {
       return PromptResponse::Deny; // don't grant permission if this fails
     }
 
+    // Lock stdio streams, so no other output is written while the prompt is
+    // displayed.
+    let _stdout_guard = std::io::stdout().lock();
+    let _stderr_guard = std::io::stderr().lock();
+
     // print to stderr so that if stdout is piped this is still displayed.
     const OPTS: &str = "[y/n] (y = yes, allow; n = no, deny)";
     eprint!("{}  ┌ ", PERMISSION_EMOJI);
@@ -238,6 +243,9 @@ impl PermissionPrompter for TtyPrompter {
       };
     };
 
+    drop(_stdout_guard);
+    drop(_stderr_guard);
+
     value
   }
 }