The present invention relates to a substrate processing apparatus for processing a substrate, such as a wafer, while supplying a cleaning liquid (e.g. pure water and a liquid chemical) to the substrate, and also relates to a pipe cleaning method for the substrate processing apparatus. The substrate processing apparatus includes: a first cleaning lane including first cleaning units (52), (54) each for cleaning a substrate while supplying pure water to the substrate; a second cleaning lane including second cleaning units (60), (62) each for cleaning a substrate while supplying pure water to the substrate; a first pure-water supply pipe (120) for supplying the pure water to the first cleaning lane; and a second pure-water supply pipe (180) for supplying the pure water to the second cleaning lane.