The operation of the cardiopulmonary bypass (CPB) system requires skilled techniques and experience. Intraoperatively, the perfusionist needs to intermittently manipulate both of the occluders on the venous- and arterial-line sides to achieve the desired blood flow rates. To facilitate the occluder operation, we propose an automatic control system for the arterial-line side blood flow rate based on a dynamic model that addresses the relationship between the occluder operation and blood flow rate in the CPB system. The simulation results demonstrated that the proposed system was able to control the blood flow rate even when the estimation error of the model parameters was presented. Then, we implemented this control system in the CPB system and conducted an experiment to automatically control the arterial-line side blood flow rate. We confirmed that the blood flow rate on the arterial-line side could follow the manually operated venous-line side blood flow rate.Clinical Relevance— The automatic blood flow rate control system for a cardiopulmonary bypass system, proposed in this paper, contributes to reducing the burden of occluder operation on a perfusionist.