A control unit 3 of a flow rate control system 1 comprises: a recording unit 31 for recording measured values of a pressure sensor P and a temperature sensor T, a storage unit 32 for storing volume data between a first valve V1 and a second valve V2 corresponding to the measured value of the pressure sensor P, and an arithmetic unit 33 for calculating a flow rate based on a first pressure value P1 and a first temperature value T1 measured after opening the first valve V1 and the second valve V2 to flow a gas and then closing the first valve V1 and the second valve V2 simultaneously in a state where the gas is flowing; a second pressure value P2 and a second temperature value T2 measured after opening the first valve V1 and the second valve V2 to flow a gas, closing the second valve V2 in a state where the gas is flowing, and then closing the first valve V1 after a predetermined time Δt has elapsed; and a volume value V between the first valve V1 and the second valve V2 which corresponds to the second pressure value P2.