An ion beam irradiation device includes a vacuum chamber that accommodates a transport tray which holds a substrate, a transport unit that transports the transport tray in the vacuum chamber in a transport direction, an ion beam irradiation unit that irradiates, with ion beams, a predetermined irradiation position in the vacuum chamber, and a position detector that detects a position of the transport tray. The transport tray includes a plurality of indices that are arranged in the transport direction to indicate portions of the transport tray. The position detector images each of the indices at a predetermined imaging position during transportation of the transport tray and detects a position of the transport tray relative to the imaging position based on the imaged index.