In the previous paper, the authors presented a new method for calculating vertical motions and wave loads of large high-speed ships with hydrofoils and developed the program code TSLAM-F_HF . The computational method of TSLAM-F_HF is based on the time-domain strip method taking account of the effects of the nonlinear hydrodynamic forces and dynamic lift of the hydrofoils. In this paper, the authors apply the program code TSLAM-F_HF to a 12 m long hydrofoil catamaran in regular head seas. The computed results show that there exists a strong nonlinearity in ship motions and wave loads due to the unsteady lift of the hydrofoils and the impact forces by the hydrofoil slamming. When we design large high-speed ships, the structural aspects are often more important than the hydrodynamical ones. The program code TSLAM-F_HF is a very useful tool for the structural design of large high-speed ships with hydrofoils. In the next step, the author simulate motions of the ships actively controlled by the hydrofoil flaps to stabilize the ship motions in order to prevent the hydrofoil emergence which leads to strong impact forces on the hydrofoils. The feedback gains for the flap control are determined by solving the optimal state regulator problem. The result shows that the flap control is very effective in stabilizing the ship motions. It reduces the amplitide of the ship motions to about 20 % of that for the non-controlled conditions and it can also prevent the hydrofoil emergence among rough seas.