A flow rate controller is provided that includes a setting flow rate shaping part that, in the case of receiving an input setting flow rate having a discontinuous point at which a target value discontinuously changes from a first target value to a second target value, outputs a shaped setting flow rate in which a continuously changing interval is inserted in place of the discontinuous point in the input setting flow rate; and a valve control part that controls a flow rate control valve opening so as to reduce a deviation between the shaped setting flow rate and a measured flow rate, wherein the setting flow rate shaping part is configured to, depending on the magnitude of an absolute deviation between the first target value and the second target value in the input setting flow rate, change a rate of change in target value in the continuously changing interval.