This research aims to identify and analyze the primary causes of overheating in the CAT 18 Auxiliary Engine aboard the AHTS Logindo Stamina vessel and to evaluate its impact on the vessel’s operational performance. Overheating has been found to significantly reduce Engine efficiency, increase fuel consumption, and potentially cause blackouts that endanger navigational safety. The investigation identified three main causes: cracking of the seawater pump cover, failure of the thermostat due to prolonged use, and clogging of the sea chest strainer by marine debris. A qualitative descriptive method was applied, involving direct observation and interviews with the ship’s Engine crew. The mitigation efforts included repairing the seawater pump cover using high-temperature-resistant Devcon adhesive, replacing the damaged thermostat, and implementing a regular Plan Maintenance System (PMS). The findings underscore the critical importance of proper cooling system management and routine maintenance discipline in preventing overheating and maintaining the reliable operation of auxiliary Engines aboard ships.