The present paper deals with a mathematical model of a heaving-buoy Wave Energy Converter (WEC) equipped with high-pressure hydraulic power take-off machinery for energy conversion. This model is based on linear hydrodynamic theory, and a hybrid frequency–time domain model is used to study the dynamics of the heaving-body exposed to an irregular incident wave. For the power take-off system, end-stop devices are provided to protect the hydraulic machinery when the buoy is exposed to severe sea states. The model also takes into account the lubricated friction force and pressure drops of orifice flow through the valves in the hydraulic system. All the forces mentioned in the hydraulic power take-off machinery have non-linear features. A complete non-linear state space model for the WEC system is presented in this study. The WEC system was numerically simulated for different cylinder lengths under a fixed volume. The effect of fluid compressibility in the cylinder has been investigated in the mathematical model. High frequency oscillations (HFOs) caused by the compressibility of the fluid are displayed in the time series and in corresponding power spectra, and variation is shown for different cylinder sizes. Piston ring and cylinder bore wear damage is estimated by using Archard’s equation on the basis of the simulation results. A comparison of these results with a performance of an identical WEC system which neglects fluid compressibility has been done in this work. It shows that although the spectral power is small, HFO can make a large contribution to both the ring and cylinder bore wear. For the purpose of wear prediction, oscillations at or below the wave frequency and HFO may be equally important.