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Fatwa CenterIs It Valid to Pray Fajr Behind an Imam Who Is Praying Dhuhr?
Question
I woke up at the time of Zuhr. When I entered the mosque, the Imam had already completed two rakats. When I joined the congregation and prayed two rakats of Fajr with him, did I do the right thing?"
Answer
All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad 
is His slave and Messenger.
Your action is valid according to a group of scholars, such as the Shafi’is and those who agree with them, who hold that a difference in intention between the imam and the follower does not invalidate the prayer.
Al-Nawawi 
said in his book al-Majmu’: “Our school [of thought] holds that a voluntary prayer is valid behind an obligatory one, and an obligatory prayer behind a voluntary one. An obligatory prayer is also valid behind a different obligatory prayer that matches it in the number of rak’at, such as Dhuhr behind Asr. And an obligatory prayer is valid behind a shorter obligatory prayer.
All of this is permissible without any disagreement among us ... But if the number of the follower’s rak’at is fewer, such as one who prays Fajr behind a four-rak’ah prayer or behind Maghrib, or who prays Maghrib behind a four-rak’ah prayer, there are two approaches reported by the scholars of Khurasan. The more correct of the two, which the scholars of Iraq decisively held, is that it is permissible ...” [End of quote]
Since you joined the imam in his last two rak’at (the third and fourth), and thus you prayed two complete rak’at with him, then recited the tashahhud and ended the prayer with his salutation. Your actions therefore matched the length of the Fajr prayer (two rak’at), with no excess and no significant deficiency.
After that, you may pray Dhuhr on your own, or in congregation if you find one.
Allah Knows best.
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