An image pickup apparatus including a pixel array including a first pixel that outputs a signal based on a light flux passed through an entire area of an exit pupil, a second pixel that outputs a signal based on a light flux passed through a part of the exit pupil, and a floating diffusion area shared by the plurality of rows adjacent to one another; and a controller that sets a first and a second accumulation periods so as to prevent them from overlapping with each other for a predetermined length of time or longer, when the first pixel read in the first scanning shares the floating diffusion area with the second pixel read in the second scanning, the first and second accumulation periods being periods for the row in which the first and the second pixel are arranged, respectively.