We are developing an endoscopic manipulator control system based on eye tracking, which uses pupil variation to improve control performance. In this paper, we propose a new approach for the control of camera zoom for an endoscopic manipulator using pupil variation, which has not been previously attempted. Before using pupil variation for the zoom function, we observed how pupil variation was related to controlling the timing for zooming in or out while a surgeon performed suturing tasks. After we confirmed the potential application for zoom control based on the variation of the size of pupil, we developed a zoom judge algorithm and integrated it into our endoscopic manipulator control system. We set up an experimental task to evaluate our proposal, and conclude that pupil variation has a significant effect on adjusting the zoom magnification for the endoscopic manipulator. Moreover, it shows better performance than zoom control by pedal input.