In this paper, the integration of a small SOFC commercial system into the fuselage of a mini Unmanned Aerial Vehicle (UAV) is presented. As a design constrain, the SOFC system has to be installed inside the UAV fuselage with the lowest possible offset, to reduce the volume and mass of the UAV. Due to the high operating temperature of the SOFC (800-1000 °C), the external temperature of the system is always about few hundred Celsius degrees. Due to this, malfunctioning of the SOFC system and hot spots on the fuselage shell can occur. For this reason, it is important to ensure a proper ventilation of the air volume inside the UAV fuselage. To deal with these issues, experimental and Computational Fluid dynamic studies were carried out to investigate for a correct SOFC system integration and operation in a confined environment. As a result, the optimal airflow for a safe operation of the SOFC system was determined and the behaviour of the temperature and air stream inside the fuselage was highlighted. In addition, NACA air intakes were designed on the basis on the experimental and numerical evidences, to provide a proper cooling of the SOFC system installed into the fuselage.