Women who are menstruating are supposed to pray only after they are certain that menses has stopped. Once they can ascertain this fact, they should perform ghusl and pray, if it is still the time of prayer.
In other words, you ought to make up a prayer-if your menses stops before its time is up. In case of menses stopping after the time, you only need to pray the next prayer.
If, therefore, you woke up to find out that you menses stopped, you ought to pray Fajr if the time still remains. If, however, the time has already expired, then you need not pray-unless you have reasons to believe that menses had stopped before the end of Fajr time.
In case of doubt, you should follow the safest principle, as far as the acts of worship are concerned, which is to make up the prayer. The same rule applies to all daily prayers.
Almighty Allah knows best.
