Recently, with the fourth industrial revolution, the research cases that search for optimal design points based on neural networks or machine learning have rapidly increased. In addition, research on optimization is continuously reported in the field of fuel cell research using hydrogen as fuel. However, in the case of optimization research, it often requires a large amount of training data, which means that it is more suitable for numerical research such as CFD simulation rather than time-consuming research such as actual experiments. As is well known, the design range of fuel cell flow channels is extremely small, ranging from hundreds of microns to several millimeters, which means the small tolerance could cause fatal performance loss. In this study, the general optimization study was further improved in terms of reliability by considering stochastic tolerances that may occur in actual industry. The optimization problem was defined to maximize stack power, which is employed as objective function, under the constraints such as pressure drop and current density standard deviation; the performance of the optimal point through general optimization was about 3.252 kW/L. In the reliability-based optimization problem, the boundary condition for tolerance was set to 0.1 mm and tolerance was assumed to occur along a normal distribution. The optimal point to secure 99% reliability for the given constraints was 2.918 kW/L, showing significantly lower performance than the general optimal point.