A hydrogen supply system includes: an electrochemical hydrogen pump including an electrolyte membrane, an anode and a cathode provided to a first and second main surfaces of the electrolyte membrane, respectively, an anode flow path and cathode flow path through which hydrogen flows, and a voltage applicator applying a voltage between the anode and cathode, pressurizing and sending hydrogen supplied to the anode via the anode flow path to the cathode by applying a voltage by the voltage applicator, and supplying the pressurized hydrogen in the cathode flow path to a hydrogen reservoir; a pressure adjuster adjusting a cathode flow path pressure; and a controller controlling the pressure adjuster and making the cathode flow path pressure higher than an anode flow path pressure before starting a hydrogen pressurization action for pressurizing and supplying hydrogen supplied to the anode flow path to the cathode flow path.