We developed a comprehensive simulation system for evaluating satellite-based navigation services in highly built-up areas; the system can accommodate Global Positioning System (GPS) multipath effects, as well as line-of-sight (LOS) and dilution of position (DOP) issues. For a more realistic simulation covering multipath and diffracted signal propagations, a 3D-ray tracing method was combined with a satellite orbit model and three-dimensional (3D) geographic information system (GIS) model. An accuracy estimation model based on a 3D position determination algorithm with a theoretical delay-locked loop (DLL) correlation computation could measure the extent to which multipath mitigation improved positioning accuracy in highly built-up areas. This system could even capture the multipath effect from an invisible satellite, one of the greatest factors in accuracy deterioration in highly built-up areas. Further, the simulation results of satellite visibility, DOP, and multipath occurrence were mapped to show the spatial distribution of GPS availability. By using object-oriented programming, our simulation system can be extended to other global navigation satellite systems (GNSSs) simply by adding the orbital information of the corresponding GNSS satellites. We demonstrated the applicability of our simulation system in an experimental simulation for Shinjuku, an area of Tokyo filled with skyscrapers.