Ammonia is being considered as a promising alternative to hydrogen fuel in solid oxide fuel cells (SOFCs) due to its stability and ease of storage and transportation. This study investigates the feasibility of using ammonia fuel in a tubular SOFC for shipborne unmanned aerial vehicles (UAVs). The paper develops a 3D model of a tubular-anode-supported SOFC single cell and conducts numerical simulations to analyze the impact of different operating conditions on SOFC performance. The study optimizes the SOFC’s performance by adjusting its working parameters and overall structure, revealing that increasing temperature and porosity enhance performance, but excessively high values can cause deterioration and instability in the cell. The study also finds that the cathode-supported (CS)-SOFC outperforms the anode-supported (AS)-SOFC, mainly due to its thicker cathode layer, providing better sealing and oxygen supply, resulting in a more uniform current density distribution. The paper provides valuable insights into the potential use of ammonia fuel for shipborne UAVs and offers a foundation for future research and development in the field of SOFCs. The results indicate that increasing the temperature and porosity of the SOFC can enhance battery performance, but excessive values can cause deterioration and instability in the cell. The study also highlights the impact of different operating conditions on SOFC performance, with a significant performance improvement observed in the range of 0.6–0.8 V. Additionally, the CS-SOFC outperforms the AS-SOFC due to its thicker cathode layer, but both have significant potential for development.