We introduce a new numerical method to model the fluid-structure interaction between a microcapsule and an external flow. An explicit finite element method is used to model the large deformation of the capsule wall, which is treated as a bidimensional hyperelastic membrane. It is coupled with a boundary integral method to solve for the internal and external Stokes flows. Our results are compared with previous studies in two classical test cases: a capsule in a simple shear flow and in a planar hyperbolic flow. The method is found to be numerically stable, even when the membrane undergoes in-plane compression,which had been shown to be a destabilizing factor for other methods. The results are in very good agreement with the literature. When the viscous forces are increased with respect to the membrane elastic forces, three regimes are found for both flow cases. Our method allows a precise characterization of the critical parameters governing the transitions.