Transformer units are one of the most significant equipment in power network and are integrated in all sectors of the grid. It is highly important to maintain a reliable operation of the transformer unit through timely diagnosis and inspection works. Frequency Response Analysis (FRA) is considered as quite efficient, non-destructive and well-standardized techniques for evaluation of mechanical conditions of the transformer. In this study, one of the most frequent fault type-inter-disk short circuit is emulated and its effect on FRA test results is analyzed. In order to realize this task, both practical and software FRA measurements are conducted on a transformer winding. Software modelling is based on a fabricated winding and a physical model is developed from the geometric and electrical properties of the winding. FRA results have showed identical anti-resonance frequencies and magnitudes for software simulated and practical measurements of frequency response. Furthermore, effect of internal short-circuit was investigated, resulting in magnitude decrease and anti-resonance shift according to amount of disks shorted. Developed software model of the winding can prospectively be used for online FRA application and further analysis of winding internal faults.