A serpentine flow channel is one of the most common and practical channel layouts for Polymer electrolyte fuel cells (PEFCs) since it ensures the removal of water produced in the cell with an acceptable parasitic load. The operating parameters such as temperature, pressure and flow distribution in the flow channel and gas diffusion layer (GDL) has a great influence on the performance of PEFCs. It is desired to have an optimum pressure drop because a certain pressure drop helps to remove excess liquid water from the fuel cell, too much of pressure drop would increase parasitic power needed for the pumping air through the fuel cell. In order to accurately estimate the pressure drop precise calculation of mass conservation is necessary. Flow crossover in the serpentine channel and GDL of PEFC has been investigated by using a transient, non-isothermal and three-dimensional numerical model. Considerable amount of cross flow through GDL is found and its influence on the pressure variation in the channel is identified. The results obtained by numerical simulation are also compared with the experimental as well as theoretical solution.