This study focuses on the corrosion problems of STS316(stainless steel 316) tube for the cooling system of PEMFC (Proton Exchange Membrane Fuel Cell) operation. Deionized water which is highly corrosive is used especially for cooling agent of PEMFC to eliminate electrical conductivity, The tensile stress analysis was performed to check the change of mechanical strength of cooling line and pH of the water was monitored for the observation of extent of corrosion at simulated PEMFC operating condition. When STS316 tube was exposed to deionized water for 500 hours, substantial cracks were found on the surface and the pH of water was decreased from 6.8 to 5.8. For prevention of corrosion problems, the STS316 was coated by three kinds of fluororesin such as PTFE, FEP and ETFE. Among the coating materials, PTFE was the most protective in corrosive environment and was maintained the mechanical strength. To lower the cost, the same experimental analyses were carried out for iron tubes and the result will be discussed in detail.