The Ranking source panel method was used to predict the flow phenomenon of a ship with a goose-neck type bulbous bow penetrating the free surface. The non-linearity of the free surface boundary condition was fully satisfied using an iterative calculation method, and the raised panel method was adopted to obtain a more stable solution at each iteration step. The panel cutting method was applied to generate a hull calculation grid at each iteration step, including the first step. At that time, the nose of the goose-neck type bulbous bow was divided by the free surface and the free surface panel was modified at each iteration step using the variable free surface panel method. Numerical calculations were performed to investigate the validity and efficiency of the applied numerical algorithm using the 3600 TEU container carrier. The computed wave resistance coefficients were compared with the experimentally achieved residual resistance coefficients.