First you have to unpair the old remote:
You can use any Apple Remote to unpair Apple TV from a remote. Note: If you lose the Apple Remote that you paired with Apple TV, a replacement remote will not work until you unpair Apple TV from the lost remote.
Press and hold the Menu and Previous/Rewind buttons on a white Apple Remote for 6 seconds, or the Menu and Left buttons on an aluminum Apple Remote for 6 seconds.
You can also use these steps:
- Choose Settings > General > Remotes from the Apple TV main menu.
- Choose Unpair Apple Remote.
When you’ve successfully unpaired a remote, Apple TV displays a broken chainlink symbol above a picture of a remote. You can now pair Apple TV with a different remote.
Or you can download the Remote App on your iPhone/Pad/Pod Touch and use that to control the Apple TV.
Read this for more.