It played its first professional season in the Russian Second Division in 2011.

On 15 June 2016, the club announced that will not participate in the professional-level competitions in the 2016–17 season.

[1] However, on 29 June 2016 the club received the professional license for the season.

[2] On 21 June 2018 it was announced that FC Syzran-2003 is dissolved because of financial problems.

[3][4] But on 1 July it was officially confirmed that FC Syzran-2003 will participate in the 2018–19 Russian Professional Football League (it ended the season in 3rd place).