diff --git a/packages/cli/src/modules/agents/repositories/agent-execution-thread.repository.ts b/packages/cli/src/modules/agents/repositories/agent-execution-thread.repository.ts
index 45a332336f4..e071c479b3d 100644
--- a/packages/cli/src/modules/agents/repositories/agent-execution-thread.repository.ts
+++ b/packages/cli/src/modules/agents/repositories/agent-execution-thread.repository.ts
@@ -146,6 +146,11 @@ export class AgentExecutionThreadRepository extends BaseRepository<AgentExecutio
 		cursor?: string,
 		filters: AgentSessionQueryFilters = {},
 	): Promise<AgentExecutionThreadPage> {
+		// SQLite timestamps can omit milliseconds, so compare them in one format.
+		const updatedAt =
+			this.manager.connection.options.type === 'postgres'
+				? 'thread.updatedAt'
+				: "STRFTIME('%Y-%m-%d %H:%M:%f', thread.updatedAt)";
 		const query = this.createQueryBuilder('thread')
 			.where('thread.projectId = :projectId', { projectId })
 			.andWhere('thread.agentId = :agentId', { agentId })
@@ -157,9 +162,9 @@ export class AgentExecutionThreadRepository extends BaseRepository<AgentExecutio
 			.take(limit + 1);
 
 		if (cursor) {
-			query.andWhere('thread.updatedAt < :cursor', { cursor: new Date(cursor) });
+			query.andWhere(`${updatedAt} < :cursor`, { cursor: new Date(cursor) });
 		}
-		this.applyListFilters(query, filters, userId);
+		this.applyListFilters(query, filters, userId, updatedAt);
 		const threads = await query.getMany();
 		const hasMore = threads.length > limit;
 		if (hasMore) threads.pop();
@@ -174,17 +179,18 @@ export class AgentExecutionThreadRepository extends BaseRepository<AgentExecutio
 		query: SelectQueryBuilder<AgentExecutionThread>,
 		filters: AgentSessionQueryFilters,
 		userId: string,
+		updatedAt: string,
 	) {
 		if (filters.scope === 'mine') {
 			query.andWhere('thread.ownerId = :userId', { userId });
 		}
 		if (filters.updatedAfter) {
-			query.andWhere('thread.updatedAt >= :updatedAfter', {
+			query.andWhere(`${updatedAt} >= :updatedAfter`, {
 				updatedAfter: filters.updatedAfter,
 			});
 		}
 		if (filters.updatedBefore) {
-			query.andWhere('thread.updatedAt <= :updatedBefore', {
+			query.andWhere(`${updatedAt} <= :updatedBefore`, {
 				updatedBefore: filters.updatedBefore,
 			});
 		}
diff --git a/packages/cli/test/integration/database/repositories/agent-execution.repository.test.ts b/packages/cli/test/integration/database/repositories/agent-execution.repository.test.ts
index 3ffa0d40f5a..ff0c6cee58f 100644
--- a/packages/cli/test/integration/database/repositories/agent-execution.repository.test.ts
+++ b/packages/cli/test/integration/database/repositories/agent-execution.repository.test.ts
@@ -2304,6 +2304,56 @@ describe('AgentExecutionRepository', () => {
 		return await repository.save(execution);
 	};
 
+	it('paginates sessions with whole-second and millisecond timestamps', async () => {
+		const newest = await createThread();
+		const middle = await createThread();
+		const oldest = await createThread();
+		for (const [id, timestamp] of [
+			[newest.id, '2026-01-03 00:00:01'],
+			[middle.id, '2026-01-03 00:00:00.500'],
+			[oldest.id, '2026-01-03 00:00:00'],
+		]) {
+			await threadRepo
+				.createQueryBuilder()
+				.update()
+				.set({ updatedAt: () => `'${timestamp}'` })
+				.where('id = :id', { id })
+				.execute();
+		}
+
+		const first = await threadRepo.findByProjectIdPaginated(projectId, agentId, viewerId, 1);
+		const second = await threadRepo.findByProjectIdPaginated(
+			projectId,
+			agentId,
+			viewerId,
+			1,
+			first.nextCursor ?? undefined,
+		);
+		const third = await threadRepo.findByProjectIdPaginated(
+			projectId,
+			agentId,
+			viewerId,
+			1,
+			second.nextCursor ?? undefined,
+		);
+		const after = await threadRepo.findByProjectIdPaginated(
+			projectId,
+			agentId,
+			viewerId,
+			10,
+			undefined,
+			{
+				updatedAfter: new Date('2026-01-03T00:00:00Z'),
+			},
+		);
+
+		expect(first.threads.map(({ id }) => id)).toEqual([newest.id]);
+		expect(second.threads.map(({ id }) => id)).toEqual([middle.id]);
+		expect(third.threads.map(({ id }) => id)).toEqual([oldest.id]);
+		expect(third.nextCursor).toBeNull();
+		expect(after.threads.map(({ id }) => id)).toEqual([newest.id, middle.id, oldest.id]);
+	});
+
 	it('filters private sessions before pagination and preserves their owner on reuse', async () => {
 		const owner = await createMember();
 		const other = await createAdmin();