Disclosed is a cleaning apparatus capable of cleaning a holding unit of a holding member that holds a substrate. The cleaning apparatus is configured to prevent a cleaning liquid from adhering to a rear-end unit of the holding member where a drying is difficult to be done, while a cleaning process is performed by spraying the cleaning liquid to the holding unit. Also disclosed are a substrate processing system that incorporates the cleaning apparatus, a cleaning method based on the cleaning apparatus, a program to perform the cleaning method, and a storage medium to store the program. The cleaning apparatus is equipped with a cleaning unit that cleans the holding unit by spraying the cleaning liquid to the holding unit, and a cover unit that covers the rear-end unit by making a back-and-forth operation with respect to the holding member.