diff --git a/packages/api/src/assistant-message-order.ts b/packages/api/src/assistant-message-order.ts
new file mode 100644
index 000000000..7a31cfcf2
--- /dev/null
+++ b/packages/api/src/assistant-message-order.ts
@@ -0,0 +1,51 @@
+interface OrderableMessage {
+  id: string;
+  parentId: string | null;
+}
+
+/**
+ * Orders thread messages so that a parent always precedes its children.
+ *
+ * The database can only order by `created_at`, which is second-granular on MySQL and SQLite. Two
+ * messages written in the same second therefore tie, and the client rebuilds the conversation tree
+ * from `parent_id`, so a child arriving before its parent corrupts the thread. Sorting here keeps
+ * the relative order of siblings from the incoming (already deterministic) list.
+ */
+export const orderMessagesByParent = <TMessage extends OrderableMessage>(messages: TMessage[]): TMessage[] => {
+  if (messages.length <= 1) return messages;
+
+  const known = new Set(messages.map((message) => message.id));
+  const childrenByParent = new Map<string | null, TMessage[]>();
+
+  for (const message of messages) {
+    // Treat a dangling parent reference as a root so the message is never dropped.
+    const parentId = message.parentId !== null && known.has(message.parentId) ? message.parentId : null;
+    const siblings = childrenByParent.get(parentId);
+    if (siblings) siblings.push(message);
+    else childrenByParent.set(parentId, [message]);
+  }
+
+  const ordered: TMessage[] = [];
+  const visited = new Set<string>();
+
+  const visit = (message: TMessage) => {
+    // Guards against a cycle introduced by corrupted data.
+    if (visited.has(message.id)) return;
+    visited.add(message.id);
+    ordered.push(message);
+    for (const child of childrenByParent.get(message.id) ?? []) {
+      visit(child);
+    }
+  };
+
+  for (const root of childrenByParent.get(null) ?? []) {
+    visit(root);
+  }
+
+  // Any message left over is part of a cycle; append it so nothing is silently lost.
+  for (const message of messages) {
+    if (!visited.has(message.id)) ordered.push(message);
+  }
+
+  return ordered;
+};
diff --git a/packages/api/src/router/assistant.ts b/packages/api/src/router/assistant.ts
index 3c7957d29..3544038a1 100644
--- a/packages/api/src/router/assistant.ts
+++ b/packages/api/src/router/assistant.ts
@@ -29,6 +29,7 @@ import {
 
 import type { createTRPCContext } from "../trpc";
 import { fetchOpenRouterGenerationTelemetryAsync } from "../assistant-generation-telemetry";
+import { orderMessagesByParent } from "../assistant-message-order";
 import { verifyAssistantGenerationAccessToken } from "../assistant-generation-access";
 import { createTRPCRouter, isDemoMode, permissionRequiredProcedure, protectedProcedure } from "../trpc";
 import { boardRouter } from "./board";
@@ -710,11 +711,13 @@ export const assistantRouter = createTRPCRouter({
     const thread = await ownedThreadAsync(ctx.db, input.threadId, ctx.session.user.id);
     const messages = await ctx.db.query.assistantMessages.findMany({
       where: eq(assistantMessages.threadId, thread.id),
-      orderBy: assistantMessages.createdAt,
+      // `created_at` is only second-granular on MySQL and SQLite, so sibling messages written in the
+      // same second tie. The id tiebreaker makes the database order at least deterministic.
+      orderBy: [asc(assistantMessages.createdAt), asc(assistantMessages.id)],
     });
     return {
       thread,
-      messages: messages.map((message) => ({
+      messages: orderMessagesByParent(messages).map((message) => ({
         id: message.id,
         parentId: message.parentId,
         format: message.format,
diff --git a/packages/api/src/test/assistant-message-order.spec.ts b/packages/api/src/test/assistant-message-order.spec.ts
new file mode 100644
index 000000000..f97ab9934
--- /dev/null
+++ b/packages/api/src/test/assistant-message-order.spec.ts
@@ -0,0 +1,63 @@
+import { describe, expect, test } from "vitest";
+
+import { orderMessagesByParent } from "../assistant-message-order";
+
+const message = (id: string, parentId: string | null) => ({ id, parentId });
+
+describe("orderMessagesByParent", () => {
+  test("keeps an already correct order untouched", () => {
+    const messages = [message("a", null), message("b", "a"), message("c", "b")];
+
+    expect(orderMessagesByParent(messages).map((entry) => entry.id)).toEqual(["a", "b", "c"]);
+  });
+
+  test("moves a child that the database returned before its parent", () => {
+    // Happens when created_at ties on MySQL/SQLite, which store whole seconds only.
+    const messages = [message("c", "b"), message("a", null), message("b", "a")];
+
+    expect(orderMessagesByParent(messages).map((entry) => entry.id)).toEqual(["a", "b", "c"]);
+  });
+
+  test("preserves sibling order from the incoming list", () => {
+    const messages = [message("root", null), message("first", "root"), message("second", "root")];
+
+    expect(orderMessagesByParent(messages).map((entry) => entry.id)).toEqual(["root", "first", "second"]);
+  });
+
+  test("keeps branches grouped under their parent", () => {
+    const messages = [
+      message("root", null),
+      message("branch-a", "root"),
+      message("branch-b", "root"),
+      message("branch-a-child", "branch-a"),
+    ];
+
+    expect(orderMessagesByParent(messages).map((entry) => entry.id)).toEqual([
+      "root",
+      "branch-a",
+      "branch-a-child",
+      "branch-b",
+    ]);
+  });
+
+  test("treats a dangling parent reference as a root instead of dropping the message", () => {
+    const messages = [message("orphan", "deleted-parent"), message("root", null)];
+
+    expect(orderMessagesByParent(messages).map((entry) => entry.id)).toEqual(["orphan", "root"]);
+  });
+
+  test("does not lose messages that form a cycle", () => {
+    const messages = [message("a", "b"), message("b", "a")];
+
+    expect(
+      orderMessagesByParent(messages)
+        .map((entry) => entry.id)
+        .toSorted(),
+    ).toEqual(["a", "b"]);
+  });
+
+  test("returns short lists unchanged", () => {
+    expect(orderMessagesByParent([])).toEqual([]);
+    expect(orderMessagesByParent([message("only", null)]).map((entry) => entry.id)).toEqual(["only"]);
+  });
+});