A system and method for reducing cathode carbon corrosion during start-up of a fuel cell stack. If a long enough period of time has gone by since the last system shutdown, then both the anode side and the cathode side of the stack will be filled with air. If the system includes split sub-stacks, then a start-up sequence uses a fast hydrogen purge through each sub-stack separately so as to minimize the time of the hydrogen/air front flowing through the anode side of the stacks. The start-up sequence then employs a slow hydrogen purge through the sub-stacks at the same time. If the time from the last shutdown is short enough where a significant amount of hydrogen still exists in the cathode side and the anode side of the sub-stacks, then the fast hydrogen purge can be eliminated, and the start-up sequence proceeds directly to the slow hydrogen purge.