In order to provide a flow rate control apparatus that estimates a flow rate actually flowing at a control point without a large amount of noise, there are provided a fluid resistor that is provided on a flow path, a downstream-side valve that is provided on a downstream side of the fluid resistor, a resistance flow rate measurement mechanism that measures a resistance flow rate that flows through the fluid resistor, and flows into a volumetric space located on the flow path between this fluid resistor and the downstream-side valve, a subject flow rate estimation part that estimates a valve flow rate based on the flow rate characteristics stored in the flow rate characteristics storage part, and a flow rate control unit that controls the downstream-side valve based on a set flow rate, and on the valve flow rate estimated by the subject flow rate estimation part.