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The jurists have stated that if a person comes and finds that the prayer has already been established, he should not engage in anything else, even the Sunnah of Fajr. Rather, he is obligated to join the imam in the obligatory Fajr prayer.
They differed on whether he should make up the Sunnah of Fajr immediately after the obligatory prayer, or whether he should delay it until the time of Duha (i.e., when the sun has risen about a spear’s length).
The stronger opinion is that it is permissible to make it up immediately after Fajr, based on what has been authentically reported from Qays ibn ‘Amr (may Allah be pleased with him) who said:
“The Messenger of Allah ﷺ saw me praying the two rak‘ahs of Fajr after the Fajr prayer, and he said: ‘What are these two rak‘ahs, O Qays?’
I said: ‘O Messenger of Allah, I had not prayed the two rak‘ahs of Fajr, so I am making them up now.’”
In Khilasat al-Badr al-Munir, it is mentioned that this hadith was narrated by al-Shafi’i, Abu Dawood, al-Tirmidhi, Ibn Majah, and al-Bayhaqi. Al-Tirmidhi and ‘Abd al-Haqq considered it weak due to a break in the chain, but al-Hakim and Ibn Hibban narrated it through a sound chain without any break. Al-Hakim said: “It is authentic according to the conditions of al-Bukhari and Muslim.”
Ibn Qudamah said in al-Mughni:
“The silence of the Prophet ﷺ indicates permissibility. Also, the Prophet ﷺ made up the Sunnah of Dhuhr after ‘Asr, and this case is similar in meaning.”
However, the Hanafi scholars held that it is not permissible to pray it immediately after Fajr due to the general prohibition of praying at this time. They cited the hadith from al-Tirmidhi, narrated from Abu Hurayrah, that the Prophet ﷺ said:
“Whoever did not pray the two rak‘ahs of Fajr, let him pray them after the sun rises.” – This hadith is not agreed upon to be authentic
Also, it is reported that Ibn ‘Umar (may Allah be pleased with him) used to make them up during the Duha time.
Ibn Qudamah said:
“This could be taken as a discouragement (karahah), and in such a case, it would be better to delay them until Duha, so as to avoid the scholarly disagreement and not contradict the general prohibition.
However, if he prays them (immediately), it is still permissible, because the hadith does not fall short of indicating permissibility.” End quote.