A beam extraction process (interruption and restart) is appropriately performed when a failure occurs during irradiation of a spot group. A charged particle irradiation system includes a synchrotron 12 and a scanning irradiation unit 15 that scans an ion beam extracted from the synchrotron over a subject. The extraction of the ion beam from the synchrotron is stopped on the basis of a beam extraction stop command. Scanning magnets 5A and 5B are controlled to change a point (spot) to be irradiated with the ion beam, while the extraction of the ion beam is stopped. The extraction of the ion beam from the synchrotron is restarted after the change of the spot to be irradiated. When a relatively minor failure in which continuous irradiation would be possible occurs during irradiation of a certain spot with the beam, the extraction of the beam is not immediately stopped.