There is provided a head control apparatus that controls the flying height of a head with respect to a disk by controlling heater current supplied to a heater for head protrusion adjustment. The head control apparatus includes: an acquisition section that acquires flying height information which is information concerning a variation in the flying height of the head; a determination section that determines whether the flying height variation is caused by a variation in atmospheric pressure based on a measured temperature and the flying height information acquired by the acquisition section; and a control section that controls, in the case where the determination section has determined that the flying height variation is caused by a variation in atmospheric pressure, heater current based on control information corresponding to the flying height variation caused by the atmospheric pressure variation.