diff --git a/src/core/checkpoints/__tests__/checkpoint.test.ts b/src/core/checkpoints/__tests__/checkpoint.test.ts
index e073c0cb92..d8e87c9710 100644
--- a/src/core/checkpoints/__tests__/checkpoint.test.ts
+++ b/src/core/checkpoints/__tests__/checkpoint.test.ts
@@ -1,4 +1,4 @@
-import { describe, it, expect, vi, beforeEach, afterEach } from "vitest"
+import { describe, it, expect, vi, beforeEach, afterEach, beforeAll, afterAll } from "vitest"
 import { Task } from "../../task/Task"
 import { ClineProvider } from "../../webview/ClineProvider"
 import { checkpointSave, checkpointRestore, checkpointDiff, getCheckpointService } from "../index"
@@ -394,11 +394,40 @@ describe("Checkpoint functionality", () => {
 			expect(service).toBeUndefined()
 		})
 
-		it("should return undefined if service is still initializing", async () => {
+		it("should handle initialization with isInitialCall flag", async () => {
+			// Test that isInitialCall=true doesn't use timeout
 			mockTask.checkpointService = undefined
-			mockTask.checkpointServiceInitializing = true
+			mockTask.checkpointServiceInitializing = false
+			mockTask.enableCheckpoints = true
+
+			// Mock the RepoPerTaskCheckpointService.create to return our mock service
+			const checkpointsModule = await import("../../../services/checkpoints")
+			vi.mocked(checkpointsModule.RepoPerTaskCheckpointService.create).mockReturnValue(mockCheckpointService)
+
+			// Call with isInitialCall=true
+			const service = await getCheckpointService(mockTask, { isInitialCall: true })
+
+			// Should create and return the service
+			expect(service).toBe(mockCheckpointService)
+			expect(mockTask.checkpointService).toBe(mockCheckpointService)
+		})
+
+		it("should handle initialization without isInitialCall flag", async () => {
+			// Test that without isInitialCall, it uses the default timeout
+			mockTask.checkpointService = undefined
+			mockTask.checkpointServiceInitializing = false
+			mockTask.enableCheckpoints = true
+
+			// Mock the RepoPerTaskCheckpointService.create to return our mock service
+			const checkpointsModule = await import("../../../services/checkpoints")
+			vi.mocked(checkpointsModule.RepoPerTaskCheckpointService.create).mockReturnValue(mockCheckpointService)
+
+			// Call without isInitialCall (defaults to false)
 			const service = await getCheckpointService(mockTask)
-			expect(service).toBeUndefined()
+
+			// Should create and return the service
+			expect(service).toBe(mockCheckpointService)
+			expect(mockTask.checkpointService).toBe(mockCheckpointService)
 		})
 
 		it("should create new service if none exists", async () => {
diff --git a/src/core/checkpoints/index.ts b/src/core/checkpoints/index.ts
index bc842c9f18..fb45b17c12 100644
--- a/src/core/checkpoints/index.ts
+++ b/src/core/checkpoints/index.ts
@@ -18,7 +18,11 @@ import { CheckpointServiceOptions, RepoPerTaskCheckpointService } from "../../se
 
 export async function getCheckpointService(
 	task: Task,
-	{ interval = 250, timeout = 15_000 }: { interval?: number; timeout?: number } = {},
+	{
+		interval = 250,
+		timeout = 15_000,
+		isInitialCall = false,
+	}: { interval?: number; timeout?: number; isInitialCall?: boolean } = {},
 ) {
 	if (!task.enableCheckpoints) {
 		return undefined
@@ -67,13 +71,25 @@ export async function getCheckpointService(
 		}
 
 		if (task.checkpointServiceInitializing) {
-			await pWaitFor(
-				() => {
+			// For initial call during task startup, don't use timeout to allow large repos to initialize
+			const waitOptions = isInitialCall ? { interval } : { interval, timeout }
+
+			try {
+				await pWaitFor(() => {
 					console.log("[Task#getCheckpointService] waiting for service to initialize")
 					return !!task.checkpointService && !!task?.checkpointService?.isInitialized
-				},
-				{ interval, timeout },
-			)
+				}, waitOptions)
+			} catch (err) {
+				// Only disable checkpoints if this is not the initial call and we hit a timeout
+				if (!isInitialCall) {
+					log("[Task#getCheckpointService] timeout waiting for service initialization, disabling checkpoints")
+					task.enableCheckpoints = false
+					return undefined
+				}
+				// For initial call, continue waiting or handle the error differently
+				throw err
+			}
+
 			if (!task?.checkpointService) {
 				task.enableCheckpoints = false
 				return undefined
diff --git a/src/core/task/Task.ts b/src/core/task/Task.ts
index c5be865731..30956aa658 100644
--- a/src/core/task/Task.ts
+++ b/src/core/task/Task.ts
@@ -1661,7 +1661,8 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 
 	private async initiateTaskLoop(userContent: Anthropic.Messages.ContentBlockParam[]): Promise<void> {
 		// Kicks off the checkpoints initialization process in the background.
-		getCheckpointService(this)
+		// For the initial call, don't use a timeout to allow large repositories to complete initialization
+		getCheckpointService(this, { isInitialCall: true })
 
 		let nextUserContent = userContent
 		let includeFileDetails = true