A gas supply system includes a flow controller, a first shutoff valve provided downstream of the flow controller, a second shutoff valve provided in a first flow passage communicating with the downstream side of the first shutoff valve, a second flow passage branching from the first flow passage, a third shutoff valve provided in the second flow passage, a pressure sensor that detects a pressure in a flow passage surrounded by the first, second, and third shutoff valves, a temperature sensor that detects a temperature in the flow passage, a volume measuring tank having a known volume connected downstream of the third shutoff valve, and a controller that obtains a volume of the flow passage by applying Boyle's law to open and closed states of the third shutoff valve and calculates the flow rate using the passage volume and outputs of the pressure and temperature sensors.