The team was previously named Burevestnik, Tomich, Sibelektromotor, Torpedo, Tomles and Manometr. The club is currently named after the river of Tom, where Tomsk is located. In the 1990s the team acquired a number of players that would help them begin their ascent out of the Russian Second Division. Viktor Sebelev, Valery Konovalov and Ruslan Akhidzhak were key players of the early part of the decade with Sergei Ageyev, Vyacheslav Vishnevskiy and Dmitry Kudinov strengthening the team as they made a run on the division championship. In 1996, the team finished 2nd in the division, just falling short of promotion to the Russian First Division. In 1997, Tomsk finally achieved a significant goal when they advanced to the First Division with a strong season. However, the team had a long way to go before they would make another run on a division title. Following promotion, the team acquired a number of new players including Sergei Zhukov, Andrei Talalaev and Mikhail Murashov to help keep the team in the First Division. However, Tomsk suffered a blow when their newly privatised sponsor, Eastern Oil Company pulled out and left the team with no sponsor. At this point, advancement was a pipe dream with survival in the tougher division becoming a priority. It was at this point that the team also had to upgrade their stadium to new standards of the league. The team played middling football for several years until the arrival of a new sponsor brought in much-needed funds and allowed the team to acquire new players and begin to compete. Third-place finishes in 2002 and 2003 left the team just short of promotion. However, the 2004 season brought new joy and Tomsk finished second in the division, earning promotion to the Russian Premier League for the 2005 season. The 2005 season saw Tomsk survive their first year in top-flight football with a 10th-place finish. In 2006, the team improved its position slightly with an 8th-place finish but in 2007, the club slipped to an 11th-place finish. The former jersey sponsor Tomskneft, a local subsidiary of Yukos, has recently been sold to new investors. Today, the team is sponsored by the regional authorities. The club's directors disclosed that the club needed to raise funds or it would go out of business due to debts of 200 million roubles in June 2009. At the end of the 2018–19 season, they qualified for the Premier League promotion play-offs, but lost to FC Ufa with an aggregate score of 1–2.
