Overhead crane is widely used in industries, however, the load fluctuation causes unsafety for people and equipment and prolongs the work execution time. To suppress load fluctuation, the input shaping (IS) method is often used for crane systems. The disadvantage of this method is that it contains a delay component that prolongs the travel time of the trolley. This paper establishes an optimization problem for optimizing the settling time for the crane system that uses the IS method. The settling time is optimized when designing the position controller of the trolley while considering the shaped input signal, the actuator effort, and overshoot constraints. The simulation results have shown the superiority of the proposed method compared to the independent design of the trolley position controller and the IS.