The blood purification system comprises: a blood treatment circuit that supplies blood of a patient to a blood purification unit and returns the blood to the patient; a drainage circuit that discharges drainage from the blood purification unit to a drainage reservoir using a drainage pump; an external drainage circuit that discharges the contents of the drainage reservoir to the outside; a weight scale that measures the weight of the drainage reservoir; and a drainage controller that, when the contents of the drainage reservoir are not being discharged to the outside by the external drainage circuit, calculates the actual flow rate of the drainage pump from a variation of the weight of the drainage reservoir measured by the weight scale and corrects the flow rate error between the actual flow rate and the target flow rate by controlling the drainage pump, and, when drainage of the drainage reservoir is discharged to the outside from the external drainage circuit, controls the drainage pump using a corrected value of the flow rate error from immediately before initiating the discharging of drainage.