After he finished playing, he was invited to struggling Admira Wacker as a manager in 2002. He saved the club from relegation, but quit in 2004.
In 2006 he was invited to FC Amkar Perm, which was also facing relegation. After an impressive run of performances, Amkar stayed in Premier League, and Rakhimov signed a 2-year contract with the club in the beginning of 2007 season.
On 6 December 2007, he signed a 3-year contract with Lokomotiv Moscow and was fired on 28 April 2009. After nineteen months, he returned to Amkar Perm.
On 28 September 2011 Amkar Perm President Gennady Shilov confirmed that the club had accepted Rakhimov's resignation.