An image pickup apparatus capable of performing favorable focusing operation when image signals are read out from an image pickup device at a high speed while flickers are occurring. Flickers are detected from image signals outputted from the image pickup device, while the image signals outputted from the image pickup device is stored. The image signals outputted from the image pickup device and the image signals stored in a first memory are synthesized depending on the flicker detection result. A position of a focus lens is adjusted by selectively using any one of the image signals outputted from the image pickup device and the synthesized image signal. When the image pickup device performs reading images in a cycle shorter than a flicker cycle, image synthesis is performed depending on the brightness of the image signals outputted from the image pickup device.