Fuel cells are highly efficient in terms of energy production, due to their high power efficiency. Solid Oxide Fuel Cells or Protonic Ceramic Fuel Cell are often proposed. The present paper aims to report on the electrochemical performance comparison between both systems by a Computational Fluid Dynamics approach. The developed model consists of mass, energy balances, and an electrochemical model that relates the fuel, air gas composition and temperature to voltage, current density, and other relevant fuel cell parameters. The electrochemical performances of SOFCs and PCFCs are analysed for several flow contigurations. The simulations show that, the flow management should be an essential key during the design optimization. In the PCFC operating conditions, steam is produced at the cathodic side and an excessive steam can involve clogging of PCFC cathode. As a result, electrochemical performance of PCFCs decreases more than SOFCs executions.