A gas supply system includes: a first flow channel connecting a first gas source and a chamber; a second flow channel connecting a second gas source and the first flow channel; a control valve, provided in the second flow channel, configured to control a flow rate of the second gas; an orifice provided downstream of the control valve and at a terminus of the second flow channel; a switching valve, provided at a connection point between the first flow channel and the terminus of the second flow channel, configured to control a supply timing of the second gas; an exhaust mechanism, connected to a flow channel between the control valve and the orifice in the second flow channel, configured to exhaust the second gas; and a controller configured to bring the control valve, the switching valve and the exhaust mechanism into operation.