A system and method for correcting a large fuel cell voltage spread for a split sub-stack fuel cell system. The system includes a hydrogen source that provides hydrogen to each split sub-stack and bleed valves for bleeding the anode side of the sub-stacks. The system also includes a voltage measuring device for measuring the voltage of each cell in the split sub-stacks. The system provides two levels for correcting a large stack voltage spread problem. The first level includes sending fresh hydrogen to the weak sub-stack well before a normal reactive bleed would occur, and the second level includes sending fresh hydrogen to the weak sub-stack and opening the bleed valve of the other sub-stack when the cell voltage spread is close to stack failure.