This paper addresses a design optimization of a gas turbine (GT) for marine applications. A gain-scheduling method incorporating a meta-heuristic optimization is proposed to optimize a thermodynamics-based model of a small GT engine. A comprehensive control system consisting of a proportional integral (PI) controller with additional proportional gains, gain scheduling, and a min-max controller is developed. The modeling of gains as a function of plant variables is presented. Meta-heuristic optimizations, namely a genetic algorithm (GA) and a whale optimization algorithm (WOA), are applied to optimize the designed control system. The results show that the WOA has better performance than that of the GA, where the WOA exhibits the minimum fitness value. Compared to the unoptimized gain, the time to reach the target of the power lever angle is significantly reduced. Optimal gain scheduling shows a stable response compared with a fixed gain, which can have oscillation effects as a controller responds. An effect of using bioethanol as a fuel has been observed. It shows that for the same input parameters of the GT dynamics model, the fuel flow increases significantly, as compared with diesel fuel, because of its low bioethanol heating value. Thus, a significant increase occurs only at the gain that depends on the fuel flow.