This paper describes a new wavelet boundary element method (WBEM) for large‐scale simulations of three‐dimensional Stokes problems. It is based on a Galerkin formulation and uses only one set of wavelet basis. A method for the efficient discretization and compression of the double‐layer integral operator of Stokes equation is proposed. In addition, a compression strategy for further reducing the setting‐up time for the sparse system matrix is also developed. With these new developments, the method has demonstrated a high matrix compression rate for problems with complicated geometries. Applications of the method are illustrated through several examples concerning the modeling of damping forces acting on MEMS resonators including a cantilever resonator oscillating in an unbounded air and a perforated plate resonator oscillating next to a fixed substrate. The numerical results clearly illustrate the efficiency and accuracy of the developed WBEM in these large‐scale Stokes flow simulations. Copyright © 2011 John Wiley & Sons, Ltd.