A tunneled planing craft is a high-speed boat with two tunnels over the hull bottom that are designed to improve the vessel’s performance. Hydrodynamic performance of tunneled planing hulls in calm-water is well-known, however, current information on wave conditions is limited. In this study, two different tunneled planing hulls with two degrees of freedom in heave and pitch motions are studied in regular waves by using the computational fluid dynamics (CFD) method based on the Unsteady Reynolds Averaged Navier-Stokes Equations (URANSE) in conjunction with k−ϵ turbulence model. The results demonstrate that tunneled planing hull motions in waves are nonlinear. In addition, it is found that the dynamic responses of heave and pitch motions as well as occurrence portability of the fly-over phenomenon significantly increases as the Froude number grows. Fly-over motions resulted in vertical motions and acceleration up to 5g, high impact pressure, and large induced drag. At a very high planing speed, after flying over the water surface, when the vessel re-enters the water, the resulting hydrodynamic load leads to a second fly-over motion. Since the fly-over is an unwanted movement with adverse effects, these results can provide a better understanding of the fly-over motion that one may consider in future design for improving the planing hull performance.