Pyrite FeS2 has long been considered a potentially ideal photovoltaic material, but solar cells utilizing pyrite exhibit low open-circuit voltages (VOC) and have failed to achieve conversion efficiencies >3 %. The recent discovery of a conductive p-type surface layer on n-type pyrite single crystals raises the intriguing possibility that the low VOC results from a leaky internal p-n junction between the surface and interior. Here, we reveal this internal junction, for the first time, through horizontal electronic transport measurements on sulfur vacancy (VS)-and Co-doped n-type pyrite single crystals. We observe a steep increase in resistance upon cooling heavily VS-doped crystals below 200 K, as the dominant charge transport crosses over from interior to surface conduction. The frequently employed two-resistor equivalent circuit model for lightly-doped pyrite crystals fails to reproduce this steep rise, but it can be accounted for, with high fidelity, by adding an internal Schottky junction resistance between the surface and the interior. The average extracted Schottky barrier height is 320 meV (varying from 130-560 meV), significantly below expectations from band bending calculations (>750 meV), but similar in magnitude to VOC values reported for pyrite heterojunction solar cells. This internal p-n junction is thus directly implicated as the origin of the long-standing low-VOC problem in pyrite.