The 2016–17 FC Krasnodar season was the 6th successive season that the club played in the Russian Premier League, the highest tier of association football in Russia. They finished the season in 4th place, reacheing the Quarterfinals of the Russian Cup and the Round of 16 of the Europa League.

On 13 September 2016, Oleg Kononov Resigned as manager, with Igor Shalimov taking over as caretaker manager. before being appointed the teams permanent manager on 6 October.

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.

Last updated: 21 May 2017.
Source: See Results
Ground: A = Away; H = Home. Result: D = Draw; L = Loss; W = Win; P = Postponed.

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