A flow controller includes a channel assembly, a pressure sensor, and a pressure control valve. The channel assembly includes a laminated substrate comprised of a plurality of substrates laminated, the laminated substrate having a surface on which a gas inlet and a gas outlet are formed, and having, inside the laminated substrate, a plurality of resistance channels not communicating with one another inside the laminated substrate as internal channels. In the flow controller, the gas inlet and the gas outlet communicate to each other to form a flow rate control channel. The pressure sensor and the pressure control valve are provided on the flow rate control channel. At least one of the resistance channels which is selected to have a desired channel resistance of the flow rate control channel is connected to the flow rate control channel as part of the flow rate control channel.