In order to reduce the cost of electricity produced by wave energy converters (WECs), the benefit of selling electricity as well as the investment costs of the structure has to be considered. This paper presents a methodology for assessing the control strategy for a WEC with respect to both energy output and structural fatigue loads. Different active and passive control strategies are implemented (proportional (P) controller, proportional-integral (PI) controller, proportional-integral-derivative with memory compensation (PID) controller, model predictive control (MPC) and maximum energy controller (MEC)), and load time-series resulting from numerical simulations are used to design structural parts based on fatigue analysis using rain-flow counting, Stress-Number (SN) curves and Miner’s rule. The objective of the methodology is to obtain a cost-effective WEC with a more comprehensive analysis of a WEC based on a combination of well known control strategies and standardised fatigue methods. The presented method is then applied to a particular case study, the Wavestar WEC, for a specific location in the North Sea. Results, which are based on numerical simulations, show the importance of balancing the gained power against structural fatigue. Based on a simple cost model, the PI controller is shown as a viable solution.