The head coaching position of the team was first assigned to Andrei Kanchelskis, who was tasked with leading the club to the Russian First Division.

[3] The first official match of the club was against FC Syzran-2003 in the second round of the Russian Cup, which after extra time Ufa lost on penalties.

Ufa made their debut in the Russian league system on 24 April 2011 with a home match against FC Tyumen.

Ufa continued to build on their initial success to the extent that, coming to the end of the season, they were equal with Neftekhimik Nizhnekamsk at the top of the table with 86 points.

The return leg was played four days later in Tomsk, and despite going down early in the match, Ufa managed to hold on to their aggregate lead; a 3–1 loss to Tom was moot.

During the 2015–16 season, the team's head coach Igor Kolyvanov was dismissed due to unsatisfactory results, and was replaced by Yevgeny Perevertaylo on October 21, 2015.

The change of coach helped Ufa, but in spring the team lost several decisive matches and before the last round of the league found itself in 15th place in the relegation zone, making Perevertaylo leave.

Sergei Tomarov was appointed acting head coach for the last match, with whom Ufa managed to beat Moscow Spartak with a score of 3:1 and retain its place in the Premier League, avoiding even the relegation play-offs.

They lost 1–0 at Ibrox, and drew 1–1 at their stadium, which caused them to be eliminated from the play-off rounds of the Europa League, short from entering the group stage.

Under the leadership of the Belarusian coach, Ufa played eight official matches in which they won two victories, drew three times and suffered three defeats before his dismissal on 28 August 2023.

[16] Ufa's return to the Russian First League was met with poor performance, leaving the club barely above the relegation zone.

[17] At the first meeting of the board in 2025, the Club announced the appointment of Omari Tetradze as the new head coach, transferring Kharlachyov to the management of the youth team.