Disclosed is a system for controlling a power trunk in a trunk-equipped vehicle, including: a motor configured to transfer power to the trunk to drive the trunk; a velocity sensing unit configured to sense a velocity of the motor; a control unit configured to compute a current trunk position and an operational velocity based on information on the velocity of the motor sensed by the velocity sensing unit and control the motor based on the computed position and the operational velocity, wherein a predetermined target velocity and the operational velocity are compared, and a difference between the target velocity and the operational velocity is compensated using a proportional integral derivative (PID) control scheme. It is possible to constantly control an open/close velocity of a power trunk regardless of a change of external environments when a power trunk is opened or closed in a vehicle having a power trunk system.