A fuel cell system that employs an injector/ejector for providing fresh hydrogen and anode recirculation gas to the anode side of a fuel cell stack. The injector/ejector is operated with a variable frequency so that the injector open time at low stack current densities is long enough to allow a pressure drop to be provided in the anode flow channels to push out water that may have accumulated therein. In one embodiment, the injector/ejector control provides a minimum pulse width per cycle and a maximum frequency so that as the stack current density decreases below a certain value the frequency decreases from the maximum frequency to maintain the pulse width constant at the minimum pulse width.