Metal corrosion and substrate contamination can be suppressed, and process quality and yield can be improved. A substrate processing apparatus comprises: a process chamber; a substrate holder; a cover part closing and opening the process chamber; a substrate holder stage; a rotary mechanism rotating the substrate holder stage; a rotation shaft inserted through the cover part and connected to the substrate holder stage and the rotary mechanism so that a first gas ejection port is formed therebetween; a first gas stagnant part surrounded by the rotary mechanism, the cover part, and the rotation shaft; a second gas ejection port formed at the substrate holder stage; a second gas stagnant part formed at the rotation shaft and communicating with the process chamber via the second gas ejection port; and a flow port formed at the rotation shaft for connecting the first and second gas stagnant parts.