The image pickup apparatus includes an image pickup element 106 including image pickup pixels photoelectrically converting an object image formed by a light flux from an image pickup optical system 202 and focus detection pixels photoelectrically converting two images formed by two divided light fluxes of the light flux from the image pickup optical system. The apparatus further includes an image generator 112 generating an image based on first pixel signals, a focus controller 112 performing focus control for the image pickup optical system based on second pixel signals. A signal processor 112 outputs signals read out from the image pickup pixels after each charge accumulation operation of the image pickup pixels for a predetermined time period as the first pixel signals, and outputs signals obtained by plural charge accumulation operations of the focus detection pixels as the second pixel signals.