In the Name of Allah, Most Gracious, Most Merciful.
All praise and thanks are due to Allah, and peace and blessings be upon His Messenger.
In this fatwa:
2- If the time has already expired, then you need not pray.
In his response to your question, Sheikh Ahmad Kutty, a senior lecturer and Islamic scholar at the Islamic Institute of Toronto, Ontario, Canada, states:
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.
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.