In the mid-1990s, Rotor was one of the strongest clubs in Russia, rivalling Spartak Moscow for the championship, yet never winning it. Rotor became the league runners-up in 1993 and 1997. They also enjoyed some success on the European stage, having eliminated Manchester United from the UEFA Cup in 1995.
In the 2000s, Rotor's results declined, and in 2004, the team finished last in the Russian Premier League. The following winter, Rotor was denied a professional licence, and chose not to participate in the amateur competitions.
In early 2009, there were fears that Rotor could go bankrupt very soon, and another club was founded that was originally supposed to be called FC Rotor. However, Rotor survived at that moment, and that new club had to rename itself FC Volgograd.
FC Rotor Volgograd were excluded from the Russian Second Division on August 4, 2009 due to financial problems. They had played 18 games and were in 13th position with 21 points at the time.
On February 8, 2010, it was announced that FC Volgograd would be renamed FC Rotor Volgograd in 2010 and, pending licensing, would play in the Russian First Division. The club was relegated back to the third-level Second Division after the 2010 season. In the 2011/12 season, they won their Second Division zone and were promoted to the second level once again.
The reserves team, called FC Rotor-d Volgograd or FC Rotor-2 Volgograd, participated in the professional competition - Russian Second Division in 1992-1993, 1998–2000 and 2004 and Russian Third League in 1994-1997. They came in 3rd place in their Second Division zone in 1993. In 2001, the reserves tournament for Russian Premier League has been re-established and the reserves team played there while the main team stayed in Premier League. In 2005, the main Rotor team played under the name of FC Rotor-2 Volgograd.