diff --git a/packages/sync-server/src/migrations.js b/packages/sync-server/src/migrations.js
deleted file mode 100644
index 8d002a4f61..0000000000
--- a/packages/sync-server/src/migrations.js
+++ /dev/null
@@ -1,39 +0,0 @@
-import path, { dirname } from 'node:path';
-import { fileURLToPath } from 'node:url';
-
-import migrate from 'migrate';
-
-import { config } from './load-config';
-
-export function run(direction = 'up') {
-  console.log(
-    `Checking if there are any migrations to run for direction "${direction}"...`,
-  );
-
-  const __dirname = dirname(fileURLToPath(import.meta.url)); // this directory
-
-  return new Promise(resolve =>
-    migrate.load(
-      {
-        stateStore: `${path.join(config.get('dataDir'), '.migrate')}${
-          config.get('mode') === 'test' ? '-test' : ''
-        }`,
-        migrationsDirectory: path.join(__dirname, '../migrations'),
-      },
-      (err, set) => {
-        if (err) {
-          throw err;
-        }
-
-        set[direction](err => {
-          if (err) {
-            throw err;
-          }
-
-          console.log('Migrations: DONE');
-          resolve();
-        });
-      },
-    ),
-  );
-}
diff --git a/packages/sync-server/src/migrations.ts b/packages/sync-server/src/migrations.ts
new file mode 100644
index 0000000000..363036e9c1
--- /dev/null
+++ b/packages/sync-server/src/migrations.ts
@@ -0,0 +1,58 @@
+import { readdir } from 'node:fs/promises';
+import path, { dirname } from 'node:path';
+import { fileURLToPath } from 'node:url';
+
+import { load } from 'migrate';
+
+import { config } from './load-config';
+
+type MigrationCallback = (err?: Error) => void;
+
+export async function run(direction: 'up' | 'down' = 'up'): Promise<void> {
+  console.log(
+    `Checking if there are any migrations to run for direction "${direction}"...`,
+  );
+
+  const __dirname = dirname(fileURLToPath(import.meta.url)); // this directory
+  const migrationsDir = path.join(__dirname, '../migrations');
+
+  try {
+    // Load all script files in the migrations directory
+    const files = await readdir(migrationsDir);
+    const migrationsModules: Record<
+      string,
+      {
+        up: (next?: MigrationCallback) => void;
+        down: (next?: MigrationCallback) => void;
+      }
+    > = {};
+
+    for (const f of files
+      .filter(f => f.endsWith('.js') || f.endsWith('.ts'))
+      .sort()) {
+      migrationsModules[f] = await import(path.join(migrationsDir, f));
+    }
+
+    return new Promise<void>((resolve, reject) => {
+      load(
+        {
+          stateStore: `${path.join(config.get('dataDir'), '.migrate')}${config.get('mode') === 'test' ? '-test' : ''}`,
+          migrations: migrationsModules,
+        },
+        (err, set) => {
+          if (err) return reject(err);
+
+          set[direction](err => {
+            if (err) return reject(err);
+
+            console.log('Migrations: DONE');
+            resolve();
+          });
+        },
+      );
+    });
+  } catch (err) {
+    console.error('Error during migration process:', err);
+    throw err;
+  }
+}
diff --git a/upcoming-release-notes/6346.md b/upcoming-release-notes/6346.md
new file mode 100644
index 0000000000..23f8d723ce
--- /dev/null
+++ b/upcoming-release-notes/6346.md
@@ -0,0 +1,6 @@
+---
+category: Bugfix
+authors: [jgranick]
+---
+
+Fix sync-server migrations to use ESM loader