The 2012–13 FC Krasnodar season was the clubs 2nd successive season in the Russian Premier League, the highest tier of football in Russia, in which they finished in 10th place. They also took part in the 2012–13 Russian Cup, getting eliminated at the last 16 stage by rivals Kuban Krasnodar.

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

The following players were registered with the RFPL and were listed by club's website as reserve players. They are eligible to play for the first team.

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

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

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

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

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

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