diff --git a/src/node/services/agentSession.ts b/src/node/services/agentSession.ts
index b15d13cc9d..5d8ab4387f 100644
--- a/src/node/services/agentSession.ts
+++ b/src/node/services/agentSession.ts
@@ -110,6 +110,7 @@ export class AgentSession {
     this.compactionHandler = new CompactionHandler({
       workspaceId: this.workspaceId,
       historyService: this.historyService,
+      partialService: this.partialService,
       emitter: this.emitter,
     });
 
diff --git a/src/node/services/compactionHandler.test.ts b/src/node/services/compactionHandler.test.ts
index c5f591de7d..8e498ae7ed 100644
--- a/src/node/services/compactionHandler.test.ts
+++ b/src/node/services/compactionHandler.test.ts
@@ -1,6 +1,7 @@
 import { describe, it, expect, beforeEach, mock } from "bun:test";
 import { CompactionHandler } from "./compactionHandler";
 import type { HistoryService } from "./historyService";
+import type { PartialService } from "./partialService";
 import type { EventEmitter } from "events";
 import { createMuxMessage, type MuxMessage } from "@/common/types/message";
 import type { StreamEndEvent } from "@/common/types/stream";
@@ -48,6 +49,26 @@ const createMockHistoryService = () => {
   };
 };
 
+const createMockPartialService = () => {
+  let deletePartialResult: Result<void, string> = Ok(undefined);
+
+  const deletePartial = mock((_) => Promise.resolve(deletePartialResult));
+  const readPartial = mock((_) => Promise.resolve(null));
+  const writePartial = mock((_, __) => Promise.resolve(Ok(undefined)));
+  const commitToHistory = mock((_) => Promise.resolve(Ok(undefined)));
+
+  return {
+    deletePartial,
+    readPartial,
+    writePartial,
+    commitToHistory,
+    // Allow setting mock return values
+    mockDeletePartial: (result: Result<void, string>) => {
+      deletePartialResult = result;
+    },
+  };
+};
+
 const createMockEmitter = (): { emitter: EventEmitter; events: EmittedEvent[] } => {
   const events: EmittedEvent[] = [];
   const emitter = {
@@ -112,6 +133,7 @@ const setupSuccessfulCompaction = (
 describe("CompactionHandler", () => {
   let handler: CompactionHandler;
   let mockHistoryService: ReturnType<typeof createMockHistoryService>;
+  let mockPartialService: ReturnType<typeof createMockPartialService>;
   let mockEmitter: EventEmitter;
   let emittedEvents: EmittedEvent[];
   const workspaceId = "test-workspace";
@@ -122,10 +144,12 @@ describe("CompactionHandler", () => {
     emittedEvents = events;
 
     mockHistoryService = createMockHistoryService();
+    mockPartialService = createMockPartialService();
 
     handler = new CompactionHandler({
       workspaceId,
       historyService: mockHistoryService as unknown as HistoryService,
+      partialService: mockPartialService as unknown as PartialService,
       emitter: mockEmitter,
     });
   });
@@ -209,6 +233,23 @@ describe("CompactionHandler", () => {
       );
     });
 
+    it("should delete partial.json before clearing history (race condition fix)", async () => {
+      const compactionReq = createCompactionRequest();
+      mockHistoryService.mockGetHistory(Ok([compactionReq]));
+      mockHistoryService.mockClearHistory(Ok([0]));
+      mockHistoryService.mockAppendToHistory(Ok(undefined));
+
+      const event = createStreamEndEvent("Summary");
+      await handler.handleCompletion(event);
+
+      // deletePartial should be called once before clearHistory
+      expect(mockPartialService.deletePartial.mock.calls).toHaveLength(1);
+      expect(mockPartialService.deletePartial.mock.calls[0][0]).toBe(workspaceId);
+
+      // Verify deletePartial was called (we can't easily verify order without more complex mocking,
+      // but the important thing is that it IS called during compaction)
+    });
+
     it("should call clearHistory() and appendToHistory()", async () => {
       const compactionReq = createCompactionRequest();
       mockHistoryService.mockGetHistory(Ok([compactionReq]));
diff --git a/src/node/services/compactionHandler.ts b/src/node/services/compactionHandler.ts
index c24c20ea10..d9d9a998ed 100644
--- a/src/node/services/compactionHandler.ts
+++ b/src/node/services/compactionHandler.ts
@@ -1,5 +1,6 @@
 import type { EventEmitter } from "events";
 import type { HistoryService } from "./historyService";
+import type { PartialService } from "./partialService";
 import type { StreamEndEvent } from "@/common/types/stream";
 import type { WorkspaceChatMessage, DeleteMessage } from "@/common/orpc/types";
 import type { Result } from "@/common/types/result";
@@ -13,6 +14,7 @@ import { log } from "@/node/services/log";
 interface CompactionHandlerOptions {
   workspaceId: string;
   historyService: HistoryService;
+  partialService: PartialService;
   emitter: EventEmitter;
 }
 
@@ -27,12 +29,14 @@ interface CompactionHandlerOptions {
 export class CompactionHandler {
   private readonly workspaceId: string;
   private readonly historyService: HistoryService;
+  private readonly partialService: PartialService;
   private readonly emitter: EventEmitter;
   private readonly processedCompactionRequestIds: Set<string> = new Set<string>();
 
   constructor(options: CompactionHandlerOptions) {
     this.workspaceId = options.workspaceId;
     this.historyService = options.historyService;
+    this.partialService = options.partialService;
     this.emitter = options.emitter;
   }
 
@@ -106,6 +110,18 @@ export class CompactionHandler {
 
     const historicalUsage = usageHistory.length > 0 ? sumUsageHistory(usageHistory) : undefined;
 
+    // CRITICAL: Delete partial.json BEFORE clearing history
+    // This prevents a race condition where:
+    // 1. CompactionHandler clears history and appends summary
+    // 2. sendQueuedMessages triggers commitToHistory
+    // 3. commitToHistory finds stale partial.json and appends it to history
+    // By deleting partial first, commitToHistory becomes a no-op
+    const deletePartialResult = await this.partialService.deletePartial(this.workspaceId);
+    if (!deletePartialResult.success) {
+      log.warn(`Failed to delete partial before compaction: ${deletePartialResult.error}`);
+      // Continue anyway - the partial may not exist, which is fine
+    }
+
     // Clear entire history and get deleted sequences
     const clearResult = await this.historyService.clearHistory(this.workspaceId);
     if (!clearResult.success) {