Provided are a fan filter unit and a sterilization apparatus capable of shortening a sterilization operation time to be performed at a changeover. The sterilization apparatus has: a working space; a fan filter unit for supplying clean air to the working space; and a sterilizing gas charging unit on the air suction side of the fan filter unit. The fan filter unit comprises: a fan unit section constituted by an air blower and a pressurization chamber; a dust removal filter provided on the downstream side of the fan unit section; a passage bypassing the dust removal filter; and an opening and closing mechanism of the passage. By opening the opening and closing mechanism, the air flow not passing through the dust removal filter can be supplied to the secondary side of the fan filter unit.