A setup system at least including a substrate processing apparatus and a test terminal is provided. The substrate processing apparatus includes a plurality of process chambers, a plurality of process chamber control units, a comprehensive control unit and an operation unit. The test terminal is connected to the plurality of process chamber control units while the comprehensive control unit and the operation unit are disconnected from the plurality of process chamber control units. The test terminal transmits a process chamber test operation command to the plurality of process chamber control units by executing a test terminal program. The setup system is capable of reducing time necessary for a setup process when starting to operate the substrate processing apparatus with the plurality of process chambers.