A wafer container cleaning device for cleaning container bodies and container covers of wafer containers includes a housing having a cleaning chamber defined therein, a rotor rotatably installed within the cleaning chamber of the housing, a plurality of container holders mounted to the rotor to removably hold the container bodies and the container covers, and a cleaning solution sprayer nozzle for spraying a cleaning solution toward the container bodies and the container covers held by the container holders. Each of the container holders includes a support tray having a body support portion for supporting each of the container bodies in an upside down state and a cover support portion for supporting each of the container covers.