Disclosed is an apparatus for controlling a wiper motor for a wiper system. The wiper motor includes a double cam plate rotated by rotational force of a motor, and internal contact points formed by a P-terminal and an E-terminal disconnected/connected by the double cam plate. The double cam plate includes a first cam plate and a second cam plate for connecting the P-terminal and the E-terminal, and a center plate between the first and second cam plates. The apparatus includes a circuit line connecting the P-terminal with an off terminal of a low relay, and a control unit turning off the low relay simultaneously when the P-terminal and the E-terminal connected by the first cam plate are disconnected when a multifunctional switch is turned off. The apparatus decreases electromotive force applied to the wiper motor while the center plate is in contact with the P-terminal.