Unreliable and inflexible analog control systems of fatigue test stands applied in laboratories are being replaced by systems enabling easy development and implementation of new test ideas. This paper presents a digital control system applied in the fatigue test stand SHM 250b. It is based on a new electronic system and the I/O board RT-DAQ4/PCI with the software Matlab/Simulink used for communication with the board. The control system for the fatigue test stand SHM 250b gives the possibility of performing fatigue tests under controlled strain ε(t), stress σ(t) and energy parameter W(t) which is calculated from the stress and strain signals. The applied control system is now used, depending on the performed fatigue tests, and can be developed for specific needs of material strength analysis.