A boundary element methodology is developed for the static analysis of three-dimensional bodies exhibiting a linear elastic material behavior coupled with microstructural effects. These microstructural effects are taken into account with the aid of a simple strain gradient elastic theory with surface energy. A variational statement is established to determine all possible classical and non-classical (due to gradient with surface energy terms) boundary conditions of the general boundary value problem. The gradient elastic fundamental solution with surface energy is explicitly derived and used to construct the boundary integral equations of the problem with the aid of the reciprocal theorem valid for the case of gradient elasticity with surface energy. It turns out that for a well posed boundary value problem, in addition to a boundary integral representation for the displacement, a second boundary integral representation for its normal derivative is also necessary. All the kernels in the integral equations are explicitly provided. The numerical implementation and solution procedure are provided. Surface quadratic quadrilateral boundary elements are employed and the discretization is restricted only to the boundary. Advanced algorithms are presented for the accurate and efficient numerical computation of the singular integrals involved. Two numerical examples are presented to illustrate the method and demonstrate its merits.