A method for operating a fuel cell stack (10) for a fuel cell system, in particular of a vehicle, in which by reversing the flow direction (14, 16) of a coolant during a cooling operation, the coolant in the fuel cell stack (10) is initially conveyed in a first direction (14). The coolant is subsequently conveyed in a second direction (16) which is at least substantially opposite to the first direction (14). A time period, after the elapse of which the flow direction (14, 16) is reversed, is changed during the cooling operation. In addition, a distance at which a coolant volume is situated from a heat source (12) that is present in the fuel cell stack (10) may be changed during the cooling operation. The invention further relates to a fuel cell system.