If your remote doesn't work during setup, try these steps.
If your remote doesn't pair automatically, press the Home
button until "Press
to start" appears on-screen (about 10 seconds).
Move your remote closer to your Fire TV device, within 10 ft (3 m).
Remove the batteries from your remote and wait 30 seconds.
Put the batteries back in and then press and hold the Home
button again.
Reset your Fire TV remote.