In hemodialysis machines peristaltic pumps are responsible for the transfer of fluids. The main characteristic of these pumps is that they can transport the solutions with significant error. That depends on the tube segment deviation caused through the production. Due to the fact that the medical fluid represents sometimes drugs and in the same time it is required to control the fluid balance of the patient, it is important to transfer these fluids as accurate as possible. The goal of the paper is to design a controller that satisfies the mentioned requirements. First, the system identification is realized by classical moving average method (ARX), followed by the design of two controllers: a classical PID one and a fuzzy controller. After comparing their simulation results, the most preferable one was implemented in practice. Real simulation results of the implemented controller end the paper.