Battery energy storage systems (BESS) are nowadays essential parts of microgrids. A thermal management system (TMS) belongs to substantial control components ensuring optimal operation and long lifespan of batteries. Advanced control strategies implemented in TMS require accurate thermal models to keep battery temperature within predefined bounds while minimizing operating costs. This paper proposes machine learning-based models to predict temperature inside real industrial BESS. Challenges represent partially continuous and partially discrete input signals. Furthermore, inner fans located inside modules affect the temperature in this particular BESS. Unfortunately, the information on fans’ operations is not available. This study also provides an accuracy analysis of bagged classification and regression trees (CART), multi-layer perceptron (MLP), and averaged neural network (avNNet). The results report high prediction accuracy, over 95%, for all models, even the ones with a more straightforward structure.