I have had this happen with one of my remotes. I just took the battery out and changed the battery again. Make sure you are putting in the battery correctly.
Fire TV Quick Tips
Hold down the Select button for 5 seconds to put the remote into pair mode.
Hold down the Select + Play buttons together for 5 seconds to Restart the device.
Restart the device: Settings > System > Restart, then once restarted unplug the power cable for 5 seconds then plug back in.