Founded in 2007, the club competes in the Ligai Olii Tojikiston, the top flight of Tajik football league system.

[3] The team had some experienced players and some young players mostly from Tajikistan national under-17 football team that won bronze in AFC U-17 Championship 2006 and reached round 16 at 2007 FIFA U-17 World Championship, winning two trophies – the traditional winter-spring tournament Rustam Doltabaev and the Tajik Cup.

[5] In the first Tajik Super Cup, defeating three-time national champion Vakhsh Qurghonteppa 2–0, following two goals from Dilshod Vasiev in extra time.

[3] In the final of the 2010 Tajik Cup, which traditionally takes place on 5 October – the birthday of the country's President Emomali Rahmon, Istiqlol with large score 5–0 defeated FK Khujand.

[6] On 20 March 2012, Istiklol's contract with Rafikov had expired at the end of the 2011 season and they had decided not to renew it, with Mubin Ergashev taking over in a caretaker capacity.

[23] After Mubin Ergashev took charge of Istiklol for their two AFC Champions League matches, Vitaliy Levchenko was appointed as the club's new manager on 17 February 2020, with Alisher Tukhtaev returning to an assistants role.

[31] On 27 June 2022, Vitaly Levchenko and his coaching staff left Istiklol after their contracts expired,[32] with Assistant Manager Alisher Tukhtaev being placed in interim charger.

[33] On 29 October 2022, Alisher Tukhtaev guided Istiklol to their ninth Tajik Cup title with a 5–3 victory on penalties over Kuktosh Rudaki after the match finished 2-2.

[38] On 11 February 2024, Istiklol announced that Igor Cherevchenko, Yuri Baturenko, Alisher Tukhtaev and Lilia Sidorkina had all left the club after their contracts had expired.

[42] On 1 November 2024, Istiklol were crowned Champions of Tajikistan for the thirteenth time, after closest challengers Khujand were defeated 1-0 by Vakhsh Bokhtar.

On 14 June 2011, a Istiklol victory after a disputed play was awarded to them by referees led to violent riots that saw 16 people injured and at least 20 arrested.

[52] In 2012, five players of rival team Ravshan Kulob were sanctioned with suspensions or fines for "unruly behavior" after defeating Istiklol 1-0.

Continental Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.