The Apostolic Prefecture of Azerbaijan is a Roman Catholic Apostolic Prefecture (missionary jurisdiction) in Baku, the capital of Azerbaijan.

It is exempt, i.e. directly subject to the Holy See, not part of any ecclesiastical province.

Its legal status is ensured by the local law of the Azerbaijan Republic and has a special status thanks to the Concordat signed by Pope John Paul II and former president Heydar Aliyev.

It was established on 11 October 2000 as Mission sui iuris of Baku, on territory split from the Apostolic Administration of the Caucasus.

On 4 August 2011, it was promoted as Apostolic Prefecture of Azerbaijan.