FC Tambov started out on the professional level in the third-tier Russian Professional Football League in the 2013–14 season. Despite coming in last in their zone in their first professional season, the team was not relegated, as a team that came ahead of them in the table dropped out for financial reasons.
For the 2016–17 season, they were promoted to the Russian Football National League for the first time. On the last day of the 2016–17 season, they needed to defeat FC SKA-Khabarovsk away to achieve 4th place and a spot in the promotion play-offs for the Russian Premier League, but the game ended with a score of 2–2, leaving Tambov in 5th place. At the end of the next 2017–18 season they secured 4th place and a chance to play in the promotion play-offs. They lost both legs of the play-offs to FC Amkar Perm and remained in the FNL.
On 11 May 2019, the club secured a top-two finish in the 2018–19 Russian National Football League and subsequently promotion to the Russian Premier League for the 2019–20 season, for the first time in the club's history.