OBJECTIVE: MRI-guided real-time transcranial magnetic stimulation (TMS) navigators that apply electromagnetic modeling have improved the utility of TMS. However, their accuracy and speed depends on the assumed volume conductor geometry. Spherical models found in present navigators are computationally fast but may be inaccurate in some areas. Realistically shaped boundary-element models (BEMs) could increase accuracy at a moderate computational cost, but it is unknown which model features have the largest influence on accuracy. Thus, we compared different types of spherical models and BEMs. METHODS: Globally and locally fitted spherical models and different BEMs with either one or three compartments and with different skull-to-brain conductivity ratios (1/1-1/80) were compared against a reference BEM. RESULTS: The one-compartment BEM at inner skull surface was almost as accurate as the reference BEM. Skull/brain conductivity ratio in the range 1/10-1/80 had only a minor influence. BEMs were superior to spherical models especially in frontal and temporal areas (up to 20mm localization and 40% intensity improvement); in motor cortex all models provided similar results. CONCLUSIONS: One-compartment BEMs offer a good balance between accuracy and computational cost. SIGNIFICANCE: Realistically shaped BEMs may increase TMS navigation accuracy in several brain areas, such as in prefrontal regions often targeted in clinical applications.