Abstract: Provided are a hydrogen compressor and a hydrogen filling system capable of increasing purity of a hydrogen gas via surely discharging oil trapped from a discharged gas and accumulated in a vessel even during operation of the compressor, and also preventing leakage of the hydrogen gas from an oil discharge pipe. The hydrogen compressor includes vessels of a snubber and a filter each arranged at a downstream side of the final compressing stage of the compressor. The hydrogen compressor further includes oil discharge pipes each connected with a bottom of each vessel, and level sensors each detecting a level of oil accumulated in each vessel. The oil discharge pipes include automatic valves configured to open/close based on detection values of the level sensors. The oil discharge pipes join to be an oil discharge pipe including a manual valve controlling an oil flow rate in the oil discharge pipe.