Quay cranes are the most expensive and important handling machine in container port operations, as the efficiency of the container terminals depends on it. This study aims to optimize the berth scheduling quay crane service and waiting times by the application of integer programming and queueing theory in identifying the actual waiting time and service time of an international container terminal in the Philippines. The paper utilizes ProModel simulation and Lindo Optimization software to evaluate the berth operation and the scheduling of quay cranes for the container terminal. Results show that the utilization of the berth operation is at 44.44% with an average waiting time of 58.18 hours per week which signifies that there is no congestion with low berth occupancy. Recommendations of the study is a process that optimized the berth and quay crane scheduling applicable to the allocation of quay crane’s workload per berthing position as the berth operation process and quay crane scheduling is optimized from 5.62 hours per day to 5.59 hours which saves 0.03 hours daily.