A three-dimensional fabricating apparatus includes a fabrication chamber, a supply chamber, a flattening unit, and a controller. In the fabrication chamber, powder is layered to form a powder layer and bonded together in a desired shape to form a layered fabrication object. The supply chamber stores the powder. The flattening unit is reciprocally movable above the supply chamber and the fabrication chamber, to transfer the powder and flatten the powder in the fabrication chamber to form the powder layer. The controller is configured to control the flattening unit to move in a first direction to transfer and supply the powder from the supply chamber to the fabrication chamber. The controller is configured to control the flattening unit to move in a second direction opposite the first direction to form the powder layer and transfer an unused portion of the powder from the fabrication chamber to the supply chamber.