Making the Second Rak‘a Longer than the First
Question
In the first rak‘a of the Fajr prayer Zayd recited the last ruku‘ of Surat al-Qalam, and in the second rak‘a he recited the whole of Surat al-Qiyama. What we wish to know is: in this case, what was in excess in the prayer and what was deficient? Kindly write in detail and with evidence, with references to the Book of Allah, the reliable books of hadith and the books of fiqh.
Answer
It is better (afdal) and mustahabb to recite a separate [complete] sura in each rak‘a. In Fajr, making the first rak‘a longer than the second is better, and the reverse is makruh — that is, making the second long and the first short. However, if in Fajr the second rak‘a occasionally turns out to be longer in an ordinary way, it is not makruh.
Source: Fatawa Mahmudiyya
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