diff --git a/extensions/codex/src/app-server/event-projector.ts b/extensions/codex/src/app-server/event-projector.ts
index 6e4f9b6264f..bfe1477fa07 100644
--- a/extensions/codex/src/app-server/event-projector.ts
+++ b/extensions/codex/src/app-server/event-projector.ts
@@ -220,6 +220,7 @@ export class CodexAppServerEventProjector {
       timedOut: false,
       idleTimedOut: false,
       timedOutDuringCompaction: false,
+      timedOutDuringToolExecution: false,
       promptError,
       promptErrorSource: promptError ? this.promptErrorSource || "prompt" : null,
       sessionIdUsed: this.params.sessionId,
diff --git a/src/agents/harness/selection.test.ts b/src/agents/harness/selection.test.ts
index 487d290ac80..7e151da17e5 100644
--- a/src/agents/harness/selection.test.ts
+++ b/src/agents/harness/selection.test.ts
@@ -68,6 +68,7 @@ function createAttemptResult(sessionIdUsed: string): EmbeddedRunAttemptResult {
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     promptError: null,
     promptErrorSource: null,
     sessionIdUsed,
diff --git a/src/agents/harness/v2.test.ts b/src/agents/harness/v2.test.ts
index b83283a5dba..d5086a017a1 100644
--- a/src/agents/harness/v2.test.ts
+++ b/src/agents/harness/v2.test.ts
@@ -47,6 +47,7 @@ function createAttemptResult(): EmbeddedRunAttemptResult {
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     promptError: null,
     promptErrorSource: null,
     sessionIdUsed: "session-1",
diff --git a/src/agents/pi-embedded-runner.run-embedded-pi-agent.auth-profile-rotation.e2e.test.ts b/src/agents/pi-embedded-runner.run-embedded-pi-agent.auth-profile-rotation.e2e.test.ts
index 7cd811b0ff6..749454ebc59 100644
--- a/src/agents/pi-embedded-runner.run-embedded-pi-agent.auth-profile-rotation.e2e.test.ts
+++ b/src/agents/pi-embedded-runner.run-embedded-pi-agent.auth-profile-rotation.e2e.test.ts
@@ -168,6 +168,7 @@ const makeAttempt = (overrides: Partial<EmbeddedRunAttemptResult>): EmbeddedRunA
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     promptError: null,
     promptErrorSource: null,
     sessionIdUsed: "session:test",
diff --git a/src/agents/pi-embedded-runner/run.overflow-compaction.fixture.ts b/src/agents/pi-embedded-runner/run.overflow-compaction.fixture.ts
index 3d4c04b2494..29bc3a19050 100644
--- a/src/agents/pi-embedded-runner/run.overflow-compaction.fixture.ts
+++ b/src/agents/pi-embedded-runner/run.overflow-compaction.fixture.ts
@@ -45,6 +45,7 @@ export function makeAttemptResult(
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     promptError: null,
     promptErrorSource: null,
     sessionIdUsed: "test-session",
diff --git a/src/agents/pi-embedded-runner/run.ts b/src/agents/pi-embedded-runner/run.ts
index cffa69daebc..c96a7622c3d 100644
--- a/src/agents/pi-embedded-runner/run.ts
+++ b/src/agents/pi-embedded-runner/run.ts
@@ -1133,6 +1133,7 @@ export async function runEmbeddedPiAgent(
             timedOut,
             idleTimedOut,
             timedOutDuringCompaction,
+            timedOutDuringToolExecution,
             sessionIdUsed,
             sessionFileUsed,
             lastAssistant: sessionLastAssistant,
@@ -1932,6 +1933,7 @@ export async function runEmbeddedPiAgent(
             failoverReason: assistantFailoverReason,
             timedOut,
             timedOutDuringCompaction,
+            timedOutDuringToolExecution,
             profileRotated: false,
           });
           const assistantFailoverOutcome = await handleAssistantFailover({
@@ -1944,6 +1946,7 @@ export async function runEmbeddedPiAgent(
             timedOut,
             idleTimedOut,
             timedOutDuringCompaction,
+            timedOutDuringToolExecution,
             allowSameModelIdleTimeoutRetry:
               timedOut &&
               idleTimedOut &&
diff --git a/src/agents/pi-embedded-runner/run/assistant-failover.test.ts b/src/agents/pi-embedded-runner/run/assistant-failover.test.ts
index 474683f97b9..db7c575ec13 100644
--- a/src/agents/pi-embedded-runner/run/assistant-failover.test.ts
+++ b/src/agents/pi-embedded-runner/run/assistant-failover.test.ts
@@ -19,6 +19,7 @@ function makeParams(overrides: Partial<Params> = {}): Params {
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     allowSameModelIdleTimeoutRetry: false,
     assistantProfileFailureReason: null,
     lastProfileId: undefined,
diff --git a/src/agents/pi-embedded-runner/run/assistant-failover.ts b/src/agents/pi-embedded-runner/run/assistant-failover.ts
index 84d3a2c2b1b..be37dde285b 100644
--- a/src/agents/pi-embedded-runner/run/assistant-failover.ts
+++ b/src/agents/pi-embedded-runner/run/assistant-failover.ts
@@ -42,6 +42,7 @@ export async function handleAssistantFailover(params: {
   timedOut: boolean;
   idleTimedOut: boolean;
   timedOutDuringCompaction: boolean;
+  timedOutDuringToolExecution: boolean;
   allowSameModelIdleTimeoutRetry: boolean;
   assistantProfileFailureReason: AuthProfileFailureReason | null;
   lastProfileId?: string;
@@ -177,6 +178,7 @@ export async function handleAssistantFailover(params: {
       failoverReason: params.failoverReason,
       timedOut: params.timedOut,
       timedOutDuringCompaction: params.timedOutDuringCompaction,
+      timedOutDuringToolExecution: params.timedOutDuringToolExecution,
       profileRotated: true,
     });
   }
diff --git a/src/agents/pi-embedded-runner/run/attempt.ts b/src/agents/pi-embedded-runner/run/attempt.ts
index f116dffa970..f5d88246fd4 100644
--- a/src/agents/pi-embedded-runner/run/attempt.ts
+++ b/src/agents/pi-embedded-runner/run/attempt.ts
@@ -101,6 +101,7 @@ import {
   resolveBootstrapPromptTruncationWarningMode,
   resolveBootstrapTotalMaxChars,
 } from "../../pi-embedded-helpers.js";
+import { countActiveToolExecutions } from "../../pi-embedded-subscribe.handlers.tools.js";
 import { subscribeEmbeddedPiSession } from "../../pi-embedded-subscribe.js";
 import { createPreparedEmbeddedPiSettingsManager } from "../../pi-project-settings.js";
 import {
@@ -782,6 +783,7 @@ export async function runEmbeddedAttempt(
   let timedOut = false;
   let idleTimedOut = false;
   let timedOutDuringCompaction = false;
+  let timedOutDuringToolExecution = false;
   let promptError: unknown = null;
   let emitDiagnosticRunCompleted:
     | ((outcome: "completed" | "aborted" | "error", err?: unknown) => void)
@@ -2250,6 +2252,14 @@ export async function runEmbeddedAttempt(
         aborted = true;
         if (isTimeout) {
           timedOut = true;
+          // Distinguish run-timer fires that occur while tool execution is in
+          // flight (LLM already responded; primary model is not at fault) from
+          // LLM-phase timeouts. Mirrors the `timedOutDuringCompaction` precedent
+          // (#46889) so the failover policy can skip pointless model fallback.
+          // Closes #52147.
+          if (!timedOutDuringCompaction && countActiveToolExecutions(params.runId) > 0) {
+            timedOutDuringToolExecution = true;
+          }
         }
         if (isTimeout) {
           runAbortController.abort(reason ?? makeTimeoutAbortReason());
@@ -3456,6 +3466,7 @@ export async function runEmbeddedAttempt(
         timedOut,
         idleTimedOut,
         timedOutDuringCompaction,
+        timedOutDuringToolExecution,
         promptError: promptError ? formatErrorMessage(promptError) : undefined,
         promptErrorSource,
         usage: attemptUsage,
@@ -3474,6 +3485,7 @@ export async function runEmbeddedAttempt(
           timedOut,
           idleTimedOut,
           timedOutDuringCompaction,
+          timedOutDuringToolExecution,
           promptError: promptError ? formatErrorMessage(promptError) : undefined,
           promptErrorSource,
           usage: attemptUsage,
@@ -3498,6 +3510,7 @@ export async function runEmbeddedAttempt(
         timedOut,
         idleTimedOut,
         timedOutDuringCompaction,
+        timedOutDuringToolExecution,
         promptError: promptError ? formatErrorMessage(promptError) : undefined,
       });
       trajectoryEndRecorded = true;
@@ -3511,6 +3524,7 @@ export async function runEmbeddedAttempt(
         timedOut,
         idleTimedOut,
         timedOutDuringCompaction,
+        timedOutDuringToolExecution,
         promptError,
         promptErrorSource,
         preflightRecovery,
@@ -3555,6 +3569,7 @@ export async function runEmbeddedAttempt(
           timedOut,
           idleTimedOut,
           timedOutDuringCompaction,
+          timedOutDuringToolExecution,
           promptError: promptError ? formatErrorMessage(promptError) : undefined,
         });
       }
diff --git a/src/agents/pi-embedded-runner/run/failover-policy.test.ts b/src/agents/pi-embedded-runner/run/failover-policy.test.ts
index c4081c5789a..bfa3c0a04c8 100644
--- a/src/agents/pi-embedded-runner/run/failover-policy.test.ts
+++ b/src/agents/pi-embedded-runner/run/failover-policy.test.ts
@@ -72,6 +72,7 @@ describe("resolveRunFailoverDecision", () => {
         failoverReason: "rate_limit",
         timedOut: false,
         timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: false,
         profileRotated: false,
       }),
     ).toEqual({
@@ -91,6 +92,7 @@ describe("resolveRunFailoverDecision", () => {
         failoverReason: "rate_limit",
         timedOut: false,
         timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: false,
         profileRotated: true,
       }),
     ).toEqual({
@@ -110,6 +112,7 @@ describe("resolveRunFailoverDecision", () => {
         failoverReason: null,
         timedOut: false,
         timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: false,
         profileRotated: false,
       }),
     ).toEqual({
@@ -134,6 +137,64 @@ describe("resolveRunFailoverDecision", () => {
     });
   });
 
+  it("does not rotate or fallback assistant timeouts that fired during tool execution (#52147)", () => {
+    expect(
+      resolveRunFailoverDecision({
+        stage: "assistant",
+        aborted: true,
+        externalAbort: false,
+        fallbackConfigured: true,
+        failoverFailure: false,
+        failoverReason: null,
+        timedOut: true,
+        timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: true,
+        profileRotated: false,
+      }),
+    ).toEqual({
+      action: "continue_normal",
+    });
+  });
+
+  it("does not fallback assistant tool-execution timeouts even after profile rotation exhausted (#52147)", () => {
+    expect(
+      resolveRunFailoverDecision({
+        stage: "assistant",
+        aborted: true,
+        externalAbort: false,
+        fallbackConfigured: true,
+        failoverFailure: false,
+        failoverReason: null,
+        timedOut: true,
+        timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: true,
+        profileRotated: true,
+      }),
+    ).toEqual({
+      action: "continue_normal",
+    });
+  });
+
+  it("still rotates assistant timeouts that fired during LLM phase (no active tool execution)", () => {
+    expect(
+      resolveRunFailoverDecision({
+        stage: "assistant",
+        aborted: true,
+        externalAbort: false,
+        fallbackConfigured: true,
+        failoverFailure: false,
+        failoverReason: null,
+        timedOut: true,
+        timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: false,
+        profileRotated: false,
+      }),
+    ).toEqual({
+      action: "rotate_profile",
+      reason: null,
+    });
+  });
+
   it("does not rotate or fallback assistant timeouts after an external abort", () => {
     expect(
       resolveRunFailoverDecision({
@@ -145,6 +206,7 @@ describe("resolveRunFailoverDecision", () => {
         failoverReason: null,
         timedOut: true,
         timedOutDuringCompaction: false,
+        timedOutDuringToolExecution: false,
         profileRotated: false,
       }),
     ).toEqual({
diff --git a/src/agents/pi-embedded-runner/run/failover-policy.ts b/src/agents/pi-embedded-runner/run/failover-policy.ts
index 841b392c01e..10c026d417c 100644
--- a/src/agents/pi-embedded-runner/run/failover-policy.ts
+++ b/src/agents/pi-embedded-runner/run/failover-policy.ts
@@ -56,6 +56,7 @@ type AssistantDecisionParams = {
   failoverReason: FailoverReason | null;
   timedOut: boolean;
   timedOutDuringCompaction: boolean;
+  timedOutDuringToolExecution: boolean;
   profileRotated: boolean;
 };
 
@@ -81,7 +82,7 @@ function shouldRotatePrompt(params: PromptDecisionParams): boolean {
 function shouldRotateAssistant(params: AssistantDecisionParams): boolean {
   return (
     (!params.aborted && (params.failoverFailure || params.failoverReason !== null)) ||
-    (params.timedOut && !params.timedOutDuringCompaction)
+    (params.timedOut && !params.timedOutDuringCompaction && !params.timedOutDuringToolExecution)
   );
 }
 
diff --git a/src/agents/pi-embedded-runner/run/types.ts b/src/agents/pi-embedded-runner/run/types.ts
index c69dd499ebd..81c850eecdf 100644
--- a/src/agents/pi-embedded-runner/run/types.ts
+++ b/src/agents/pi-embedded-runner/run/types.ts
@@ -58,6 +58,12 @@ export type EmbeddedRunAttemptResult = {
   idleTimedOut: boolean;
   /** True if the timeout occurred while compaction was in progress or pending. */
   timedOutDuringCompaction: boolean;
+  /**
+   * True if the run-level timer fired while at least one tool execution was
+   * still in flight. The LLM had already responded; the timeout is unrelated
+   * to the primary model and must not trigger model fallback. Closes #52147.
+   */
+  timedOutDuringToolExecution: boolean;
   promptError: unknown;
   /**
    * Identifies which phase produced the promptError.
diff --git a/src/agents/pi-embedded-subscribe.handlers.tools.ts b/src/agents/pi-embedded-subscribe.handlers.tools.ts
index 5673e2f952d..f4d1707165a 100644
--- a/src/agents/pi-embedded-subscribe.handlers.tools.ts
+++ b/src/agents/pi-embedded-subscribe.handlers.tools.ts
@@ -92,6 +92,26 @@ function buildToolStartKey(runId: string, toolCallId: string): string {
   return `${runId}:${toolCallId}`;
 }
 
+/**
+ * Count tool executions currently in flight for a given run.
+ *
+ * Reads the existing `toolStartData` map: handleToolExecutionStart inserts on
+ * tool start, handleToolExecutionEnd deletes on completion. Used by the
+ * embedded run timer to detect whether a run-level timeout fired while tool
+ * execution was active (in which case the failover policy should not rotate
+ * to a fallback model — the LLM had already responded).
+ */
+export function countActiveToolExecutions(runId: string): number {
+  const prefix = `${runId}:`;
+  let count = 0;
+  for (const key of toolStartData.keys()) {
+    if (key.startsWith(prefix)) {
+      count += 1;
+    }
+  }
+  return count;
+}
+
 function isCronAddAction(args: unknown): boolean {
   if (!args || typeof args !== "object") {
     return false;
diff --git a/src/agents/test-helpers/pi-embedded-runner-e2e-fixtures.ts b/src/agents/test-helpers/pi-embedded-runner-e2e-fixtures.ts
index 185c6af2a24..8c6de735916 100644
--- a/src/agents/test-helpers/pi-embedded-runner-e2e-fixtures.ts
+++ b/src/agents/test-helpers/pi-embedded-runner-e2e-fixtures.ts
@@ -109,6 +109,7 @@ export function makeEmbeddedRunnerAttempt(
     timedOut: false,
     idleTimedOut: false,
     timedOutDuringCompaction: false,
+    timedOutDuringToolExecution: false,
     promptError: null,
     promptErrorSource: null,
     sessionIdUsed: "session:test",
diff --git a/src/trajectory/export.ts b/src/trajectory/export.ts
index 8f3b9d7a17d..441c6a53e33 100644
--- a/src/trajectory/export.ts
+++ b/src/trajectory/export.ts
@@ -745,6 +745,8 @@ function buildArtifactsCapture(params: {
     idleTimedOut: runtimeArtifacts?.idleTimedOut ?? runtimeEnd?.idleTimedOut,
     timedOutDuringCompaction:
       runtimeArtifacts?.timedOutDuringCompaction ?? runtimeEnd?.timedOutDuringCompaction,
+    timedOutDuringToolExecution:
+      runtimeArtifacts?.timedOutDuringToolExecution ?? runtimeEnd?.timedOutDuringToolExecution,
     promptError:
       runtimeArtifacts?.promptError ?? runtimeEnd?.promptError ?? runtimeCompletion?.promptError,
     promptErrorSource: runtimeArtifacts?.promptErrorSource ?? runtimeCompletion?.promptErrorSource,
diff --git a/src/trajectory/metadata.test.ts b/src/trajectory/metadata.test.ts
index ec56b2fc4a8..ef3aa3cde45 100644
--- a/src/trajectory/metadata.test.ts
+++ b/src/trajectory/metadata.test.ts
@@ -185,6 +185,7 @@ describe("trajectory metadata", () => {
       timedOut: false,
       idleTimedOut: false,
       timedOutDuringCompaction: false,
+      timedOutDuringToolExecution: false,
       compactionCount: 1,
       assistantTexts: ["done"],
       finalPromptText: "run tests",
diff --git a/src/trajectory/metadata.ts b/src/trajectory/metadata.ts
index f3bbcf22a79..755763ff3f0 100644
--- a/src/trajectory/metadata.ts
+++ b/src/trajectory/metadata.ts
@@ -46,6 +46,7 @@ type BuildTrajectoryArtifactsParams = {
   timedOut: boolean;
   idleTimedOut: boolean;
   timedOutDuringCompaction: boolean;
+  timedOutDuringToolExecution: boolean;
   promptError?: string;
   promptErrorSource?: string | null;
   usage?: unknown;
@@ -303,6 +304,7 @@ export function buildTrajectoryArtifacts(
     timedOut: params.timedOut,
     idleTimedOut: params.idleTimedOut,
     timedOutDuringCompaction: params.timedOutDuringCompaction,
+    timedOutDuringToolExecution: params.timedOutDuringToolExecution,
     promptError: params.promptError,
     promptErrorSource: params.promptErrorSource,
     usage: params.usage,