The Neftchi Baku 2012–13 season is Neftchi Baku's 21st Azerbaijan Premier League season, and their third season under manager Boyukagha Hajiyev. Neftchi participated in the Second and Third UEFA Champions League qualifying rounds, defeating FC Zestafoni of Georgia in the Second round before losing to Ironi Kiryat Shmona of Israel in the Third round. This meant that they dropped down into the 2012–13 UEFA Europa League Play Off Round, where they defeated APOEL of Cyprus 4-2 on aggregate to qualify for the group stages of the Europa League for the first time. In the group stages they were drawn against FK Partizan of Serbia, Rubin Kazan of Russia and Internazionale of Italy. They also won the Azerbaijan Premier League for the 3rd time in a row, and completed a domestic double by defeating Khazar Lankaran on penalties in the Azerbaijan Cup final.

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.