The main purpose of this research is to design a high-fatigue performance hoop wrapped compressed natural gas (CNG) composite cylinder. To this end, an optimization algorithm was presented as a combination of finite element simulation (FES) and response surface analysis (RSA). The geometrical model was prepared as a variable wall-thickness following the experimental measurements. Next, transient dynamic analysis was performed subjected to the refueling process, including the minimum and maximum internal pressures of 20 and 200 bar, respectively. The time histories of stress tensor components were extracted in the critical region. Furthermore, RSA was utilized to investigate the interaction effects of various polymer composite shell manufacturing process parameters (thickness and fiber angle) on the fatigue life of polymer composite CNG pressure tank (type-4). In the optimization procedure, four parameters including wall-thickness of the composite shell in three different sections of the CNG tank and fiber angle were considered as input variables. In addition, the maximum principal stress of the component was considered as the objective function. Eventually, the fatigue life of the polymer composite tank was calculated using stress-based failure criterion. The results indicated that the proposed new design (applying optimal parameters) leads to improve the fatigue life of the polymer composite tank with polyethylene liner about 2.4 times in comparison with the initial design.