Modern agricultural operations now demand the utilisation of a wide variety of equipment and specialist machinery systems, with many having rotary elements such as axles, gears, pulleys etc. With these agricultural machinery systems which have rotary elements, uncontrolled vibrations may become an important problem to consider. When the initial ‘switch-on’ frequency meets with the natural frequency of a machine element in the system, undesired noise, high levels of vibration and mechanical failures may occur during operation. In this regard, it is important to predict natural frequency modes of the elements under loading as a result of these vibrations. Computing capability and design software tools are able to assist design and analysis engineers to predict and evaluate natural and forced frequency modes of these elements. These computer aided applications in the engineering domain are typically referred to as Computer Aided Engineering (CAE) and have been used with success in industry for a long time. Hence, it can be shown that the use of CAE applications in the design and analysis processes of agricultural machinery systems could be beneficial. In this study, a finite element modal analysis on the larger pulley of a fodder crushing machine which was manufactured by a commercial company in Turkey, is presented. The torque and cycle of the pulley shaft measurements of the machine were conducted and the data used in the Finite Element Analysis (FEA) to simulate resonance frequency modes. As a conclusion of the study, resonance frequency simulations were conducted and the results have been presented. Additionally, suggestions for reducing the undesired effect of vibration for the agricultural machinery systems are given.