This study is about flow channels in the design of the PEM (Proton Exchange Membrane) fuel cell system. In the experimental study, different flow geometry, Nafion membrane, and bipolar plate gas diffusion channel designs are available. In some cases, the techno economic analysis method is applied. Cost analysis for the design has also been made and compared with similar studies. It was obtained that the new flow channel design increased the PEM fuel cell performance. A unit energy cost was set to 42.6 [$/W]. When a similar system was implemented for a year, the annual energy cost was calculated to be 25.48 [$/y]. The aim of this study is to determine the cost benefit analysis of PEM fuel cell with a combined flow channel design. In addition, the simple payback period was found to be 0.81 [y]. Thus, the PEM fuel cell was determined by the techno economic analysis calculation, in which energy savings can be achieved by the flow channel design.