Boundary element methods (BEM) represent a powerful computational approach for modeling wave-structure interactions essential to wave energy converter design and analysis. This chapter presents a rigorous examination of BEM techniques, their mathematical foundations, and their specific applications in wave energy systems. By focusing computation exclusively on boundary surfaces rather than entire fluid domains, BEM offers significant computational efficiency advantages for solving linear and weakly nonlinear hydrodynamic problems, making it particularly valuable in the iterative design optimization processes required for effective wave energy harvesting systems. The chapter is structured to provide comprehensive coverage across five interconnected sections. The introduction to boundary element methods establishes the fundamental mathematical principles underlying BEM, explaining the Green’s function formulation, boundary integral equations, and the method’s strengths in handling infinite and semi-infinite domains without discretization of the entire fluid region. The second section explores BEM specifically in wave-structure interactions, detailing the linear potential flow theory, radiation-diffraction problems, and the calculation of hydrodynamic coefficients critical for modeling how wave energy converters respond to incident waves. Numerical implementation of BEM forms the technical core of the chapter, covering mesh generation techniques, singularity treatment approaches, solution methods for resulting linear systems, and acceleration techniques that enhance computational efficiency. The application section demonstrates how BEM serves as the foundation for frequency-domain and time-domain models of various wave energy converter types, examining its role in device performance prediction, optimization processes, and array layout design. The final section addresses current challenges in BEM applications, including limitations in modeling extreme waves and strongly nonlinear effects, while exploring emerging hybrid methods, high-order formulations, and coupling techniques with other numerical approaches that promise to extend BEM capabilities for next-generation wave energy converter designs.