Disclosed herein is a wafer processing system for processing wafers one at a time, the wafer processing system including: a plurality of trays each configured to accommodate a wafer; a conveyor configured to transfer the wafers accommodated in the trays; first and second tray holding apparatuses arranged to be spaced from each other along the conveyor, the first and second tray holding apparatuses unloading the trays from the conveyor and loading the unloaded trays onto the conveyor; and first and second apparatuses provided for the first and second tray holding apparatuses, respectively, the first and second apparatuses including a processing unit configured to process the wafers transferred by the conveyor, and a loading/unloading unit configured to unload a wafer from or load a wafer onto one of the trays that is held by the first or second tray holding apparatus.