After Rakhimov 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 three-year contract with
FC 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. On 5 September 2018, he rejoined
FC Akhmat Grozny (the team was called Terek during his previous time at the club). He resigned from Akhmat on 30 September 2019 with club in 15th place. In 2016–17 season, he sent Akhmat to 5th place, which is still the highest ever record in the club's history. On 11 October 2020, Rakhimov was appointed as head coach of
FC Ufa. He resigned from Ufa on 3 April 2021, following a 0–4 loss to
FC Dynamo Moscow, with the club still in the same relegation-zone 15th place it was in when Rakhimov took over as manager. On 12 April 2023, Rakhimov was hired by
Rubin Kazan. On 20 May 2023, Rubin secured promotion back to the
Russian Premier League after one season at the second tier. On 28 May 2024, Rakhimov's contract with Rubin was extended to June 2026. On 13 January 2026, Rubin sacked Rakhimov, with the club in 7th place in the Premier League. == Managerial statistics ==