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.
Any person who misses an obligatory prayer should make it up in the same way; he would have performed it at its prescribed fixed time. So, you first pray the Sunnah of Fajr and then pray the Fajr obligatory prayer.
Abu Hurayrah narrated: “We stayed overnight with the Prophet in a journey and we did not wake up till sunrise. The Prophet said: “Every man should take his mount (camel, horse….) and move away from this place as Satan has joined us here (in this place).”
Abu Hurayrah said: “We did what the Prophet said.” Then, he (the Prophet) asked for some water and did his ablutions. Then he performed two Rak’ahs before the Fajr Iqamah was called.”
What the Prophet prayed first was the Fajr Sunnah.
Allah knows best.