A substrate processing apparatus includes a substrate holder, a first cleaning body, a first moving mechanism, a second cleaning body, a second moving mechanism, and a controller. The first cleaning body cleans one of the upper surface and the lower surface of the substrate held by the substrate holder by ejecting fluid thereto or by coming into contact therewith. The second cleaning body cleans the other one of the upper surface and the lower surface of the substrate held by the substrate holder by coming into contact therewith. The controller controls the first moving mechanism and the second moving mechanism to perform a both-surface cleaning processing in which the first cleaning body which ejects the fluid to one surface or is in contact with the upper surface and the second cleaning body which is in contact with the lower surface are horizontally moved in synchronization with each other.