An image pickup apparatus includes an image pickup element 10 that includes unit cells capable of individually reading signals from pixels that receive light beams transmitting through different pupil positions of an image pickup lens 5, a detector 20 that generates a pair of image signals in a pupil division direction using a signal from a pixel corresponding to each of the unit cells to perform focus detection based on a phase difference, a defective pixel storage unit 22 that stores defective pixel information, and a defective pixel compensating unit 20 that compensates a signal of a defective pixel based on an output of the defective pixel storage unit. The defective pixel compensating unit 20 compensates the signal of the defective pixel using a signal obtained from a pixel disposed in a direction different from the pupil division direction with respect to the defective pixel.