The invention relates to a system for controlling a hydrofoil boat comprising at least three static pressure or dynamic pressure and water speed sensors submerged in the water and located on the submerged hydrofoils of the boat, an electronic controller on the boat, an actuator for each one of the submerged hydrofoils able to change an angle of attack of its respective hydrofoil. The control system allows boats on hydrofoils to sail in a safe and comfortable way in any wave condition within the sailing limits of traditional boats.