Let's properly define what this capacity is that you're talking about.
It is the amount of (usable) energy you can extract from the battery of fuel cell.
Battery capacity is specified in Amp-hour where 1 Ah is 1 Ampere of current for 1 hour. For the energy you will also need the cell's voltage because only voltage times current gives you power. So a 3.7 V 1 Ah battery can supply 3.7 V * 1 A = 3.7 W for 1 hour or 3.7 WattHour (3.7 Whr). 3.7 W equals 3.7 Joule/second, 1 hour is 3600 seconds, so 3.7 * 3600 = 13320 Joules. That is the amount of energy you can extract from that battery !
You can do something similar with a fuel cell. I am unfamiliar with fuel cell specifications but I'm guessing it will have a specification for efficiency (how much of the energy in it's fuel it can extract) or amounts of power (in Watts) it can supply given a certain fuel consumption rate.
It all depends on what you know about the fuel cell and then you can do the calculation. It should be possible to end up at the amount of Joules you can extract from the cell, assuming you have the required data.