A focused ion beam system is offered which can make a focal adjustment without relying on the structure of a sample while suppressing damage to the sample to a minimum. Also, a method of making this focal adjustment is offered. The focused ion beam system has an ion source for producing an ion beam, a lens system for focusing the beam onto the sample, a detector for detecting secondary electrons emanating from the sample, and a controller for controlling the lens system. The controller is operative to provide control such that the sample is irradiated with the ion beam without scanning the beam and that a focus of the ion beam is varied by varying the intensity of the objective lens during the ion beam irradiation. Also, the controller measures the intensity of a signal indicating secondary electrons emanating from the sample while the intensity of the objective lens is being varied. Furthermore, the controller makes a focal adjustment of the ion beam on the basis of the intensity of the objective lens obtained when the measured intensity of the signal indicating secondary electrons is minimal.