diff --git a/packages/agent/src/harness/session/jsonl/repo.ts b/packages/agent/src/harness/session/jsonl/repo.ts
index 78c0788cb..017efd1bc 100644
--- a/packages/agent/src/harness/session/jsonl/repo.ts
+++ b/packages/agent/src/harness/session/jsonl/repo.ts
@@ -85,9 +85,9 @@ export class JsonlSessionRepo
 				cwd,
 				...(options.parentSessionId === undefined ? {} : { parentSessionId: options.parentSessionId }),
 			};
-			// TODO: do we want to make session creation atomic?
-			storage = await JsonlStorage.create({ fileSystem: this.fileSystem, path, now: this.now }, header, context);
-			await storage.commit(
+			storage = await JsonlStorage.create(
+				{ fileSystem: this.fileSystem, path, now: this.now },
+				header,
 				[
 					setValue(laneLeaf("main"), null),
 					setValue(laneState("main"), { currentOperationId: null, pendingNextRun: [] }),
diff --git a/packages/agent/src/harness/session/jsonl/storage.ts b/packages/agent/src/harness/session/jsonl/storage.ts
index 9dff8e516..77896fa24 100644
--- a/packages/agent/src/harness/session/jsonl/storage.ts
+++ b/packages/agent/src/harness/session/jsonl/storage.ts
@@ -75,6 +75,10 @@ function parseTransaction(line: string): CommittedWrite[] {
 	return (Array.isArray(value) ? value : [value]).map(parseCommittedWrite);
 }
 
+function serializeTransaction(writes: readonly CommittedWrite[]): string {
+	return JSON.stringify(writes.length === 1 ? writes[0] : writes);
+}
+
 function splitCompleteLines(content: string): { lines: string[]; torn: boolean } {
 	if (content.endsWith("\n")) return { lines: content.slice(0, -1).split("\n"), torn: false };
 	const lastNewline = content.lastIndexOf("\n");
@@ -135,13 +139,16 @@ export class JsonlStorage implements Storage {
 	static async create(
 		options: JsonlStorageOptions,
 		header: JsonlStorageHeader,
+		initialWrites: Write[],
 		context: Context,
 	): Promise<JsonlStorage> {
-		fileValue(
-			await options.fileSystem.writeFile(options.path, `${JSON.stringify(header)}\n`, context),
-			`Failed to create JSONL storage ${options.path}`,
-		);
-		return new JsonlStorage(options, header, { kind: "v4" });
+		const storage = new JsonlStorage(options, header, { kind: "v4" });
+		const prepared = storage.storageState.prepareCommit(initialWrites, storage.now());
+		const lines = [JSON.stringify(header)];
+		if (prepared.writes.length !== 0) lines.push(serializeTransaction(prepared.writes));
+		await publishFileAtomically(options.fileSystem, options.path, `${lines.join("\n")}\n`, context);
+		storage.storageState.applyValidated(prepared.writes);
+		return storage;
 	}
 
 	/** Atomically create storage from a complete prepared snapshot. */
@@ -232,11 +239,7 @@ export class JsonlStorage implements Storage {
 		const prepared = this.storageState.prepareCommit(writes, this.now());
 		if (prepared.writes.length !== 0) {
 			fileValue(
-				await this.fileSystem.appendFile(
-					this.path,
-					`${JSON.stringify(prepared.writes.length === 1 ? prepared.writes[0] : prepared.writes)}\n`,
-					context,
-				),
+				await this.fileSystem.appendFile(this.path, `${serializeTransaction(prepared.writes)}\n`, context),
 				`Failed to append JSONL storage ${this.path}`,
 			);
 		}
diff --git a/packages/agent/test/harness/jsonl-session-repo.test.ts b/packages/agent/test/harness/jsonl-session-repo.test.ts
index a467b0f60..87fb46c06 100644
--- a/packages/agent/test/harness/jsonl-session-repo.test.ts
+++ b/packages/agent/test/harness/jsonl-session-repo.test.ts
@@ -1,5 +1,5 @@
 import { describe, expect, it } from "vitest";
-import { BACKGROUND_CONTEXT } from "../../src/harness/context.ts";
+import { BACKGROUND_CONTEXT, type Context } from "../../src/harness/context.ts";
 import { NodeExecutionEnv } from "../../src/harness/env/nodejs.ts";
 import { JSONL_STORAGE_VERSION, JsonlSessionRepo } from "../../src/harness/session/jsonl/index.ts";
 import { getOrThrow } from "../../src/harness/types.ts";
@@ -7,6 +7,26 @@ import { createTempDir } from "./session-test-utils.ts";
 
 const NOW = 1_700_000_000_000;
 
+class AtomicPublicationNodeExecutionEnv extends NodeExecutionEnv {
+	publication:
+		| { sourcePath: string; destinationPath: string; destinationExisted: boolean; stagedContent: string }
+		| undefined;
+
+	override async renameFile(sourcePath: string, destinationPath: string, context: Context) {
+		const destinationExists = await super.exists(destinationPath, context);
+		const stagedContent = await super.readTextFile(sourcePath, context);
+		if (destinationExists.ok && stagedContent.ok) {
+			this.publication = {
+				sourcePath,
+				destinationPath,
+				destinationExisted: destinationExists.value,
+				stagedContent: stagedContent.value,
+			};
+		}
+		return super.renameFile(sourcePath, destinationPath, context);
+	}
+}
+
 describe("JsonlSessionRepo cwd-scoped lifecycle", () => {
 	it("persists metadata and filters discovery by cwd", async () => {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
@@ -46,6 +66,45 @@ describe("JsonlSessionRepo cwd-scoped lifecycle", () => {
 		await repo.close(BACKGROUND_CONTEXT);
 	});
 
+	it("atomically publishes the header and initialized main lane", async () => {
+		const fileSystem = new AtomicPublicationNodeExecutionEnv({ cwd: createTempDir() });
+		const repo = new JsonlSessionRepo({ fileSystem, sessionsRoot: "sessions", now: () => NOW });
+		const session = await repo.create({ id: "session", cwd: "/workspace" }, BACKGROUND_CONTEXT);
+
+		const publication = fileSystem.publication;
+		if (publication === undefined) throw new Error("Expected atomic session publication");
+		expect(publication.destinationPath).toBe(session.metadata.path);
+		expect(publication.destinationExisted).toBe(false);
+		const lines = publication.stagedContent.trimEnd().split("\n");
+		expect(lines).toHaveLength(2);
+		expect(JSON.parse(lines[0]!)).toMatchObject({ kind: "header", id: "session" });
+		expect(JSON.parse(lines[1]!)).toEqual([
+			{
+				kind: "value",
+				op: "set",
+				seq: 1,
+				namespace: "pi.lane.leaf",
+				key: "main",
+				value: null,
+			},
+			{
+				kind: "value",
+				op: "set",
+				seq: 2,
+				namespace: "pi.lane.state",
+				key: "main",
+				value: { currentOperationId: null, pendingNextRun: [] },
+			},
+		]);
+		expect(getOrThrow(await fileSystem.readTextFile(session.metadata.path, BACKGROUND_CONTEXT))).toBe(
+			publication.stagedContent,
+		);
+		expect(getOrThrow(await fileSystem.exists(publication.sourcePath, BACKGROUND_CONTEXT))).toBe(false);
+
+		await session.close(BACKGROUND_CONTEXT);
+		await repo.close(BACKGROUND_CONTEXT);
+	});
+
 	it("keeps fork destinations claimed until close and rejects deleting open sessions", async () => {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
 		const repo = new JsonlSessionRepo({ fileSystem, sessionsRoot: "sessions", now: () => NOW });
diff --git a/packages/agent/test/harness/jsonl-storage-conformance.test.ts b/packages/agent/test/harness/jsonl-storage-conformance.test.ts
index 525a007a8..26535843b 100644
--- a/packages/agent/test/harness/jsonl-storage-conformance.test.ts
+++ b/packages/agent/test/harness/jsonl-storage-conformance.test.ts
@@ -37,6 +37,7 @@ registerConformance(
 				createdAt: NOW,
 				cwd: "/workspace",
 			},
+			[],
 			BACKGROUND_CONTEXT,
 		);
 		return {
diff --git a/packages/agent/test/harness/jsonl-storage.test.ts b/packages/agent/test/harness/jsonl-storage.test.ts
index a6e3db74e..09b890c99 100644
--- a/packages/agent/test/harness/jsonl-storage.test.ts
+++ b/packages/agent/test/harness/jsonl-storage.test.ts
@@ -125,7 +125,7 @@ describe("JsonlStorage persistence", () => {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
 		const options = { fileSystem, path: "list-delete.jsonl", now: () => NOW };
 		const events = storedValues.list<string>("test.events");
-		const storage = await JsonlStorage.create(options, header("list-delete"), BACKGROUND_CONTEXT);
+		const storage = await JsonlStorage.create(options, header("list-delete"), [], BACKGROUND_CONTEXT);
 		await storage.commit(
 			[storedValues.appendList(events, "first"), storedValues.appendList(events, "second")],
 			BACKGROUND_CONTEXT,
@@ -144,7 +144,7 @@ describe("JsonlStorage persistence", () => {
 	it("writes one line per transaction and replays stamped state", async () => {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
 		const options = { fileSystem, path: "session.jsonl", now: () => NOW };
-		const storage = await JsonlStorage.create(options, header("round-trip"), BACKGROUND_CONTEXT);
+		const storage = await JsonlStorage.create(options, header("round-trip"), [], BACKGROUND_CONTEXT);
 		const committed = await storage.commit(
 			[
 				sessionWrites.insertEntry({
@@ -218,7 +218,7 @@ describe("JsonlStorage snapshots", () => {
 	it("captures one serialized boundary between commits", async () => {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
 		const options = { fileSystem, path: "session.jsonl", now: () => NOW };
-		const storage = await JsonlStorage.create(options, header("snapshot"), BACKGROUND_CONTEXT);
+		const storage = await JsonlStorage.create(options, header("snapshot"), [], BACKGROUND_CONTEXT);
 
 		const firstCommit = storage.commit(
 			[
@@ -265,7 +265,7 @@ describe("JsonlStorage torn tail", () => {
 	async function seed() {
 		const fileSystem = new NodeExecutionEnv({ cwd: createTempDir() });
 		const options = { fileSystem, path: "session.jsonl" as const, now: () => NOW };
-		const storage = await JsonlStorage.create(options, header("torn"), BACKGROUND_CONTEXT);
+		const storage = await JsonlStorage.create(options, header("torn"), [], BACKGROUND_CONTEXT);
 		await storage.commit([entryWrite("kept")], BACKGROUND_CONTEXT);
 		await storage.close(BACKGROUND_CONTEXT);
 		const prefix = getOrThrow(await fileSystem.readTextFile("session.jsonl", BACKGROUND_CONTEXT));