A fuel cell watercraft includes: a hull; an electric motor serving as a power source adapted to generate propulsion of the hull; a fuel cell unit adapted to supply electric power to the electric motor; a hydrogen fuel tank adapted to supply hydrogen fuel to the fuel cell unit; a secondary battery serving as an auxiliary power supply for the fuel cell unit; and power regulation means for regulating the electric power supplied to the electric motor, in which the hull includes first and second storage spaces isolated from each other, the first and second storage spaces include equipment hatches able to be opened and closed by lid members, the fuel cell unit and the hydrogen fuel tank are housed in the first storage space, and the secondary battery and the power regulation means are housed in the second storage space.