Heart assist devices provide mechanical circulatory support for patients with end-stage heart failure. Extracorporeal blood pumps are applied to adult and pediatric patients in the case of uni- and biventricular assistance. Modern driving units provide more mobility what is an immense benefit to the quality of life of the patients. The treated heart assist device in this article is the EXCOR system (Berlin Heart GmbH, Germany), which is a pneumatically driven extracorporeal assist device. It allows uni- and biventricular heart support. The automatic control system should match the pump output to the metabolic needs by controlling the piston movement and the enclosed air mass in the pneumatic system. This paper describes the design of a control system for the extracorporeal assist device. A developed model is used for controller synthesis. This model is based on modified basic physical equations and optimized for practical applications.