The 2012–13 FC Anzhi Makhachkala season was the 3rd successive season that the club played in the Russian Premier League, the highest tier of football in Russia.

Anzhi Makhachkala finished the season in Third place, qualifying for the 2013–14 UEFA Europa League Group stage, whilst they also where Runners Up to CSKA Moscow in the Russian Cup and reached the Round of 16 of the 2012–13 UEFA Europa League where they were knocked out by Newcastle United.

Anzhi Makhachkala's away game against Zenit St. Petersburg on 10 December was played behind closed doors.

[1] Anzhi Makhachkala's home UEFA Europa League knockout phase games where played at the Luzhniki Stadium in Moscow instead of their regular Dynamo Stadium in Makhachkala, due to security issues involving the city of Makhachkala and the autonomous republic of Dagestan.

[2] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.