diff --git a/codex-rs/app-server/src/bespoke_event_handling.rs b/codex-rs/app-server/src/bespoke_event_handling.rs
index c63103161f..dae06b7236 100644
--- a/codex-rs/app-server/src/bespoke_event_handling.rs
+++ b/codex-rs/app-server/src/bespoke_event_handling.rs
@@ -769,6 +769,14 @@ pub(crate) async fn apply_bespoke_event_handling(
                 server_name: request.server_name.clone(),
                 request: request_body,
             };
+            let pause_incremented =
+                match conversation.increment_out_of_band_elicitation_count().await {
+                    Ok(_) => true,
+                    Err(err) => {
+                        error!("failed to pause timeout accounting for MCP elicitation: {err}");
+                        false
+                    }
+                };
             let (pending_request_id, rx) = outgoing
                 .send_request(ServerRequestPayload::McpServerElicitationRequest(params))
                 .await;
@@ -781,6 +789,7 @@ pub(crate) async fn apply_bespoke_event_handling(
                     conversation,
                     thread_state,
                     permission_guard,
+                    pause_incremented,
                 )
                 .await;
             });
@@ -1772,8 +1781,14 @@ async fn on_mcp_server_elicitation_response(
     conversation: Arc<CodexThread>,
     thread_state: Arc<Mutex<ThreadState>>,
     permission_guard: ThreadWatchActiveGuard,
+    pause_incremented: bool,
 ) {
     let response = receiver.await;
+    if pause_incremented
+        && let Err(err) = conversation.decrement_out_of_band_elicitation_count().await
+    {
+        error!("failed to resume timeout accounting after MCP elicitation: {err}");
+    }
     resolve_server_request_on_thread_listener(&thread_state, pending_request_id).await;
     drop(permission_guard);
     let response = mcp_server_elicitation_response_from_client_result(response);
diff --git a/codex-rs/core/src/session/mcp.rs b/codex-rs/core/src/session/mcp.rs
index 25d95e30ea..144cf6f738 100644
--- a/codex-rs/core/src/session/mcp.rs
+++ b/codex-rs/core/src/session/mcp.rs
@@ -218,6 +218,10 @@ impl Session {
             };
         }
 
+        let _pending_elicitation = turn_context
+            .turn_metadata_state
+            .track_pending_mcp_elicitation();
+
         let (tx_response, rx_response) = oneshot::channel();
         let prev_entry = {
             let mut active = self.active_turn.lock().await;
diff --git a/codex-rs/core/src/session/mod.rs b/codex-rs/core/src/session/mod.rs
index d43724e5db..b20e024ebe 100644
--- a/codex-rs/core/src/session/mod.rs
+++ b/codex-rs/core/src/session/mod.rs
@@ -1145,6 +1145,10 @@ impl Session {
         self.out_of_band_elicitation_paused.subscribe()
     }
 
+    pub(crate) fn is_out_of_band_elicitation_paused(&self) -> bool {
+        *self.out_of_band_elicitation_paused.borrow()
+    }
+
     pub(crate) fn set_out_of_band_elicitation_pause_state(&self, paused: bool) {
         self.out_of_band_elicitation_paused.send_replace(paused);
     }
diff --git a/codex-rs/core/src/tools/code_mode/mod.rs b/codex-rs/core/src/tools/code_mode/mod.rs
index ad746a1de2..986cbb3053 100644
--- a/codex-rs/core/src/tools/code_mode/mod.rs
+++ b/codex-rs/core/src/tools/code_mode/mod.rs
@@ -184,7 +184,7 @@ pub(super) async fn handle_runtime_response(
     max_output_tokens: Option<usize>,
     started_at: std::time::Instant,
 ) -> Result<FunctionToolOutput, String> {
-    let script_status = format_script_status(&response);
+    let script_status = format_script_status(exec, &response);
 
     match response {
         RuntimeResponse::Yielded { content_items, .. } => {
@@ -228,8 +228,14 @@ fn sanitize_runtime_image_detail(turn: &TurnContext, items: &mut [FunctionCallOu
     sanitize_image_detail_items(can_request_original_image_detail(&turn.model_info), items);
 }
 
-fn format_script_status(response: &RuntimeResponse) -> String {
+fn format_script_status(exec: &ExecContext, response: &RuntimeResponse) -> String {
     match response {
+        RuntimeResponse::Yielded { cell_id, .. }
+            if exec.session.is_out_of_band_elicitation_paused()
+                || exec.turn.turn_metadata_state.has_pending_mcp_elicitation() =>
+        {
+            format!("Script running with cell ID {cell_id}\nWaiting for user input")
+        }
         RuntimeResponse::Yielded { cell_id, .. } => {
             format!("Script running with cell ID {cell_id}")
         }
diff --git a/codex-rs/core/src/turn_metadata.rs b/codex-rs/core/src/turn_metadata.rs
index 0a1f781b38..15be4295e2 100644
--- a/codex-rs/core/src/turn_metadata.rs
+++ b/codex-rs/core/src/turn_metadata.rs
@@ -4,6 +4,7 @@ use std::sync::Arc;
 use std::sync::Mutex;
 use std::sync::RwLock;
 use std::sync::atomic::AtomicBool;
+use std::sync::atomic::AtomicUsize;
 use std::sync::atomic::Ordering;
 
 use serde_json::Value;
@@ -99,9 +100,21 @@ pub(crate) struct TurnMetadataState {
     turn_started_at_unix_ms: Arc<RwLock<Option<i64>>>,
     responsesapi_client_metadata: Arc<RwLock<BTreeMap<String, String>>>,
     user_input_requested_during_turn: Arc<AtomicBool>,
+    pending_mcp_elicitations: Arc<AtomicUsize>,
     enrichment_task: Arc<Mutex<Option<JoinHandle<()>>>>,
 }
 
+pub(crate) struct PendingMcpElicitationGuard {
+    count: Arc<AtomicUsize>,
+}
+
+impl Drop for PendingMcpElicitationGuard {
+    fn drop(&mut self) {
+        let previous = self.count.fetch_sub(1, Ordering::AcqRel);
+        debug_assert!(previous > 0, "pending MCP elicitation count underflowed");
+    }
+}
+
 impl TurnMetadataState {
     #[allow(clippy::too_many_arguments)]
     pub(crate) fn new(
@@ -142,6 +155,7 @@ impl TurnMetadataState {
             turn_started_at_unix_ms: Arc::new(RwLock::new(None)),
             responsesapi_client_metadata: Arc::new(RwLock::new(BTreeMap::new())),
             user_input_requested_during_turn: Arc::new(AtomicBool::new(false)),
+            pending_mcp_elicitations: Arc::new(AtomicUsize::new(0)),
             enrichment_task: Arc::new(Mutex::new(None)),
         }
     }
@@ -203,6 +217,17 @@ impl TurnMetadataState {
             .store(true, Ordering::Relaxed);
     }
 
+    pub(crate) fn track_pending_mcp_elicitation(&self) -> PendingMcpElicitationGuard {
+        self.pending_mcp_elicitations.fetch_add(1, Ordering::AcqRel);
+        PendingMcpElicitationGuard {
+            count: Arc::clone(&self.pending_mcp_elicitations),
+        }
+    }
+
+    pub(crate) fn has_pending_mcp_elicitation(&self) -> bool {
+        self.pending_mcp_elicitations.load(Ordering::Acquire) > 0
+    }
+
     pub(crate) fn set_responsesapi_client_metadata(
         &self,
         responsesapi_client_metadata: HashMap<String, String>,
diff --git a/codex-rs/core/tests/suite/code_mode.rs b/codex-rs/core/tests/suite/code_mode.rs
index 26c041d8f7..721d65e914 100644
--- a/codex-rs/core/tests/suite/code_mode.rs
+++ b/codex-rs/core/tests/suite/code_mode.rs
@@ -3,6 +3,7 @@
 use anyhow::Result;
 use base64::Engine;
 use base64::engine::general_purpose::STANDARD as BASE64_STANDARD;
+use codex_config::types::AppToolApproval;
 use codex_config::types::McpServerConfig;
 use codex_config::types::McpServerTransportConfig;
 use codex_core::config::Config;
@@ -12,6 +13,7 @@ use codex_features::CurrentTimeSource;
 use codex_features::Feature;
 use codex_login::CodexAuth;
 use codex_models_manager::bundled_models_response;
+use codex_protocol::config_types::ApprovalsReviewer;
 use codex_protocol::config_types::WebSearchMode;
 use codex_protocol::dynamic_tools::DynamicToolCallOutputContentItem;
 use codex_protocol::dynamic_tools::DynamicToolFunctionSpec;
@@ -479,6 +481,125 @@ async fn run_code_mode_turn_with_rmcp_config(
     Ok((test, second_mock))
 }
 
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn code_mode_reports_pending_mcp_elicitation_on_yield_and_wait() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let server = responses::start_mock_server().await;
+    let rmcp_test_server_bin = stdio_server_bin()?;
+    let mut builder = test_codex().with_config(move |config| {
+        let _ = config.features.enable(Feature::CodeMode);
+        let _ = config.features.enable(Feature::ToolCallMcpElicitation);
+        config.approvals_reviewer = ApprovalsReviewer::User;
+        let mut servers = config.mcp_servers.get().clone();
+        servers.insert(
+            "rmcp".to_string(),
+            McpServerConfig {
+                auth: Default::default(),
+                transport: McpServerTransportConfig::Stdio {
+                    command: rmcp_test_server_bin,
+                    args: Vec::new(),
+                    env: None,
+                    env_vars: Vec::new(),
+                    cwd: None,
+                },
+                environment_id: "local".to_string(),
+                enabled: true,
+                required: false,
+                supports_parallel_tool_calls: false,
+                disabled_reason: None,
+                startup_timeout_sec: Some(Duration::from_secs(10)),
+                tool_timeout_sec: None,
+                default_tools_approval_mode: Some(AppToolApproval::Prompt),
+                enabled_tools: None,
+                disabled_tools: None,
+                scopes: None,
+                oauth: None,
+                oauth_resource: None,
+                tools: HashMap::new(),
+            },
+        );
+        config
+            .mcp_servers
+            .set(servers)
+            .expect("test mcp servers should accept any configuration");
+    });
+    let test = builder.build(&server).await?;
+    wait_for_mcp_server(&test.codex, "rmcp").await?;
+
+    responses::mount_sse_once(
+        &server,
+        sse(vec![
+            ev_response_created("resp-1"),
+            ev_custom_tool_call(
+                "call-1",
+                "exec",
+                r#"// @exec: {"yield_time_ms": 1000}
+await tools.mcp__rmcp__sync({});"#,
+            ),
+            ev_completed("resp-1"),
+        ]),
+    )
+    .await;
+    let initial_yield = responses::mount_sse_once(
+        &server,
+        sse(vec![
+            ev_response_created("resp-2"),
+            responses::ev_function_call(
+                "call-2",
+                "wait",
+                &serde_json::to_string(&serde_json::json!({
+                    "cell_id": "1",
+                    "yield_time_ms": 10,
+                }))?,
+            ),
+            ev_completed("resp-2"),
+        ]),
+    )
+    .await;
+    let later_wait = responses::mount_sse_once(
+        &server,
+        sse(vec![
+            ev_assistant_message("msg-1", "waiting"),
+            ev_completed("resp-3"),
+        ]),
+    )
+    .await;
+
+    test.submit_turn_with_approval_and_permission_profile(
+        "request confirmation from code mode",
+        AskForApproval::OnRequest,
+        PermissionProfile::Disabled,
+    )
+    .await?;
+
+    let initial_items = custom_tool_output_items(&initial_yield.single_request(), "call-1");
+    assert_eq!(initial_items.len(), 1);
+    assert_regex_match(
+        concat!(
+            r"(?s)\A",
+            r"Script running with cell ID 1\n",
+            r"Waiting for user input\n",
+            r"Wall time \d+\.\d seconds\nOutput:\n\z"
+        ),
+        text_item(&initial_items, /*index*/ 0),
+    );
+
+    let wait_items = function_tool_output_items(&later_wait.single_request(), "call-2");
+    assert_eq!(wait_items.len(), 1);
+    assert_regex_match(
+        concat!(
+            r"(?s)\A",
+            r"Script running with cell ID 1\n",
+            r"Waiting for user input\n",
+            r"Wall time \d+\.\d seconds\nOutput:\n\z"
+        ),
+        text_item(&wait_items, /*index*/ 0),
+    );
+
+    Ok(())
+}
+
 #[cfg_attr(windows, ignore = "no exec_command on Windows")]
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn code_mode_can_return_exec_command_output() -> Result<()> {