An apparatus and method for punching a hole in a paper with a punching unit in a paper post-processing apparatus. The paper is nipped and transported with a transporting roller system arranged downstream of the punching unit in a paper transport direction to make at least a leading edge of the paper pass through an aligning unit. An actuator is activated to end the nipping of the paper by the transporting roller system, and the aligning unit aligns the paper in a width direction thereof that is perpendicular to the paper transport direction. The activation of the actuator is ended to resume the nipping of the paper, and a stopper member is inserted into a paper transport path upstream of a punch of the punching unit. A trailing edge of the paper is then caused to hit the stopper member, and the paper is punched by the punching unit.