An apparatus for a self-cleaning litter box having a control system for a mechanical self-cleaning mechanism. The litter box has a turret carrying a rake. The box includes an animal sensor that detects the presence of an animal in the box. A specified time after the animal leaves the box, the turret sweeps the rake through the litter, picks up the collected waste, and carries it to a waste bin, where the waste is dumped. The litter box is controlled by a processor executing a software program that monitors the instruments and sensors and controls the turret and rake motors. The software, in various embodiments, controls the rake motor and turret motor to execute a scoop sequence, a startup sequence, and a go home sequence.