This communication proposes an efficient boundary-integral-based “windowed Green function” (WGF) methodology for the numerical solution of 3-D general electromagnetic problems containing dielectric waveguides. The approach, which generalizes a recently introduced 2-D version of the method, provides a highly effective solver for such problems. In particular, using an auxiliary integral representation, the proposed method is able to accurately model incident mode excitation. On the basis of a smooth window function, the integral operators along the infinite waveguide boundaries are smoothly truncated, resulting in errors that decay faster than any negative power of the window size.