An apparatus for controlling an autonomous vehicle brake, including a first brake controller configured to control a brake module of an autonomous vehicle by receiving a deceleration command from an autonomous controller for controlling autonomous driving of the autonomous vehicle, and a second brake controller configured to control the brake module of the autonomous vehicle by receiving a deceleration command from the autonomous controller. The first and second brake controllers exchange monitoring information with each other in a predetermined communication manner to monitor an operation state, so that control of the brake module is transferred according to the result of monitoring.