Shaikh Ibn ul-‘Uthaymeen rahimahullah was asked:

Question:

A man missed the fajr prayer with the congregation. Does he pray the Raatibah [the Sunnah] or the obligation knowing that the congregation has left?

Answer:

He precedes the Raatibah over the obligation because the Sunnah of fajr is before the obligation. (This is the case) even if the congregants have left the Masjid

[Majmoo’ al-Fatawa wa Rasaail question  no. 868]

Translated by

Faisal Ibn Abdul Qaadir Ibn Hassan
Abu Sulaymaan