In a substrate cleaning apparatus, first cleaning solution is applied onto a substrate from a cleaning nozzle and the substrate is scrubbed with a brush, whereby the substrate is cleaned. While cleaning of the substrate is not performed, second cleaning solution is applied to the brush from a cleaning solution nozzle provided in a container to clean the brush. Since the second cleaning solution used in the substrate cleaning apparatus is almost neutral at hydrogen ion exponent pH of 6.5, and a zeta potential of the brush in the second cleaning solution has the same polarity as a zeta potential of particles which have adhered to the brush while cleaning the substrate, it is possible to efficiently remove particles adhering to the brush during cleaning of the substrate with suppressing deterioration of the brush.