An increase in wave energy converter (WEC) efficiency requires not only consideration of the nonlinear effects in the WEC dynamics and the power take-off (PTO) mechanisms, but also more integrated treatment of the whole system, i.e., the buoy dynamics, the PTO system, and the control strategy. It results in an optimization formulation that has a nonquadratic and nonstandard cost functional. This article presents the application of real-time nonlinear model predictive controller (NMPC) to two degrees of freedom point absorber type WEC with highly nonlinear PTO characteristics. The nonlinear effects, such as the fluid viscous drag, are also included in the plant dynamics. The controller is implemented on a real-time target machine, and the WEC device is emulated in real-time using the WECSIM toolbox. The results for the successful performance of the design are presented for irregular waves under linear and nonlinear hydrodynamic conditions.