A procedure for purging a fuel cell system at start-up or shutdown comprises directing the organic fuel, along with air, into a burner to produce a gas that is essentially inert to the fuel cell, such as a gas of nitrogen, carbon dioxide and water vapor. That inert gas is passed through either or both the fuel cell and fuel processing system components, such as a reformer and shift converter, to purge those components of undesirable gases. In the case of shutdown, after the cell has been disconnected from the primary load, the inert gas produced in the burner is passed either in series or in parallel through the fuel cell and fuel processing system.