In 1989, Atari released a second version of the Lynx with a number of improvements including an extra hour of battery life, a sharper LCD screen, a button to switch off the backlight (to save on battery power when games are paused), a Power LED (it blinked when the battery was low) and rubber grips on the back, all encased in a smaller more rectangle-looking black casing.

The Lynx II was backward-compatible with all Lynx games and was later advertised as being able to communicate directly with the upcoming 64-bit Jaguar.