Question: If one misses the Witr prayer and wakes up and prays the Fajr prayer, must they repeat the Witr prayer and the Fajr prayer or just the Witr prayer?
Answer:
In the Name of Allah, the Most Merciful and Compassionate,
The Witr and Fajr prayers must be repeated, only if you recalled the missed Witr prayer while performing Fajr. [Tahtawi/Shurunbulali, Hashiyat Maraqi al-Falah]
If you only recalled the missed Witr prayer after the Fajr prayer was completed, you must only repeat the Witr prayer. [Ibid.]
The Reasoning
The reason behind this ruling is the obligation of praying all prayers in the proper sequence. This applies to missed prayers as well as current ones. [Ibid.]
This rule dictates that you must make up your missed Witr before performing the next prayer as Witr comes first in order. If you do not pray Witr first, the Fajr prayer is invalid. [Ibid.]
Exceptions
There are three exceptions to the above reasoning. They are as follows:
(1) If the time of the current prayer will end or enter into a disliked time, you are allowed and possibly required to perform the current prayer first. There is no virtue in missing another prayer while trying to make up a previous one. [Ibid.]
(2) If you performed the current prayer not remembering the missed prayer that is due, the current prayer is valid. Forgetting is seen as a legal excuse in this case. [Ibid.]
(3 Lastly, if the amount of missed prayers reaches 6 obligatory prayers then it is no longer obligatory to regard the order of the prayers. Thus the current prayer is valid even though there are missed prayers due. This is because it would be an undue hardship, in this case, to have to pray all missed prayers first before the current prayer. [Ibid.]
I hope this helps,
Allah knows best.
[Shaykh] Yusuf Weltch
Checked and Approved by Shaykh Faraz Rabbani