Earthquakes that have occurred in our country and various countries around the world over the past 30 years have clearly indicated that the complex relationship between the soil, structure, and earthquake requires further research. This situation has shown that building behavior under dynamic loads can vary depending on parameters such as structural geometry, foundation soil system characteristics, and earthquake characteristics. Due to the fact that near-fault movements contain higher accelerations and higher velocity components compared to far-fault movements, high-rise structures may exhibit relatively more sensitive behavior under such loads and may be negatively affected by these earthquake contents. In this context, the aim of this study is to investigate the dynamic behavior of a 12-story building system under near-fault and far-fault ground motions, taking into account different soil properties. To this end, three-dimensional finite element models were first created for the 12-story building system, considering both fixed and flexible foundation conditions. Modal analyses were performed using finite element models created with ANSYS software, and the obtained mode periods were compared with those obtained from analytical models. Subsequently, the dynamic behavior of the 12-story building system was investigated using relative displacement, stress, and acceleration responses obtained from time-domain analyses conducted for different soil systems and fixed foundation conditions. Comparisons of the dynamic responses showed that the structural dynamic responses could be influenced not only by the soil-structure interaction system but also by nearby and distant fault earthquakes.