A substrate processing apparatus has a substrate rotating device 10, 20 for holding and rotating a substrate W, a cleaning device 41 configured to clean a substrate W which is rotated by the substrate rotating device 10, 20 at predetermined rotating speed, a movement device 42 configured to move the cleaning device 41 between a cleaning position P3 and a separate position P2, and a control unit 64. The control unit 64 controls the movement device 42 so that the cleaning device 41 located at the separate position P2 starts moving toward the cleaning position P3 before a rotating speed of the substrate W held by the substrate rotating device 10, 20 reaches the predetermined rotating speed and the cleaning device 41 reaches the cleaning position P3 after a rotating speed of the substrate W reaches the predetermined rotating speed. Therefore, it is possible to improve the throughput in the substrate cleaning step.