Istiklol Dushanbe was established in November 2007, under the Presidency of Shohruh Saidov. In 2008, Istiklol competed in the Dushanbe Group of the Second Division under head coach Kanoat Latifov, winning all 30 league games with a +154 goal difference and winning promotion to the Tajik League.[2]
In 2010, under coach Alimzhon Rafikov the team won the Super Cup,[3] the national cup and league.[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.[5] Following victory in the 2010 Tajik League, FC Istiqlol qualified for the first time for both the CIS Cup and the 2011 AFC President's Cup.[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.[7]
On 22 November 2015, Manuel Bleda scored the club's 500th league goal.[9] Istiklol's 4–2 victory over Barki Tajik on 17 April 2016, saw the club stretch their unbeaten run in the Tajik League to 40 games, with their last defeat occurring in November 2013 against Khayr Vahdat. During this run Istiklol have scored 146 goals, conceding just 17.[10] Also, the team was qualified for the 2015 AFC Cup final against Johor Darul Ta'zim F.C. of Malaysia, in which both teams were the finalist for the first time in the competition. Istiklol were defeated by the team with the score of 1–0 on the home soil in Dushanbe.
On 10 July 2016, Istiklol fired their entire coaching staff, including manager Mubin Ergashev.[11] Three days later, 13 July 2016, Istiklol announced Nikola Lazarevic as their new manager.[12]
On 25 September 2016, Istiklol suffered their first League defeat since 3 November 2013, a stretch of 51 games, 2–1 away to Ravshan Kulob.[13] On 29 October 2016, Istiklol defeated Barki Tajik 5–1, to claim their fifth Tajik League title.[14] Two days later, 31 October 2016, Istiklol announced that they had appointed Mukhsin Mukhamadiev for the 2017 season.[15] On 18 September 2017, Istiklol defeated Panjshir 5–0 to secure their sixth Tajik League title.[16] On 18 October 2017, Istiklol drew 2–2 with Bengaluru in the second leg of their Inter-zone play-off final, progressing to the final of the AFC Cup for the second time in three seasons.[17] On 4 November 2017, Istiklol were defeated 1–0 by Al-Quwa Al-Jawiya thanks to a second half Emad Mohsin goal.[18]
After being knocked out of the 2018 AFC Cup at the group stage, manager Mukhsin Mukhamadiev resigned as manager six-days later on 22 May 2018, with Alisher Tukhtaev being appointed as acting head coach.[19]
On 3 December 2018, Khakim Fuzailov was announced as Istiklol's new manager.[20] Fuzailov resigned as manager of Istiklol on 27 June 2019 after they failed to progress from the group stages of the AFC Cup, with Alisher Tukhtaev being appointed as Caretaker Manager in his place.[21] On 27 September 2019, Istiklol beat Kuktosh 6–1, to secure their eighth Tajik League title.[22] On 24 November 2019, Istiklol won 4–2 penalties to clinch their eighth Tajik Cup title.[23]
On 10 September 2020, the 2020 AFC Cup was cancelled.[26] 10 days later, 20 September 2020, Istiklol drew 1–1 with Khatlon to secure their ninth league title and seventh in a row.[27]
On 21 June 2021, Ryota Noma scored the club's 800th league goal.[31] On 21 November 2021, Istiklol defeated Dushanbe-83 8–0 to secure their 10th league title, and 8th in a row.[32]
On 27 June 2022, Vitaly Levchenko and his coaching staff left Istiklol after their contracts expired,[33] with Assistant Manager Alisher Tukhtaev being placed in interim charger.[34]
On 18 January 2023, Igor Cherevchenko was appointed as the new Head Coach of Istiklol on a one-year contract.[37]
On 1 November 2023, Istiklol defeated Ravshan Kulob 4–2 on penalties in the 2023 Tajikistan Cup Final, after an initial 1–1 draw, to claim their 10th Tajikistan Cup title.[38] A month later, on 1 December 2023, Istiklol defeated Kuktosh Rudaki 4–1 to secure their 10th league title in a row, and 12th overall.[39]
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.[40] On 15 March 2024, Istiklol announced that Nikola Lazarevic had been appointed as their new Head Coach on a one-year contract.[41]
On 4 October 2024, Istiklol announced the return of Igor Cherevchenko as their Head Coach after Nikola Lazarevic had left his role as Head Coach in mid September 2024.[43] 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.[44]
Istiklol was founded[52] and is said to be owned by Rustam Emomali, the son and heir apparent of the President of Tajikistan, Emomali Rahmon,[53] who also served captain of the team until 2012. 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.[53] In 2012, five players of rival team Ravshan Kulob were sanctioned with suspensions or fines for "unruly behavior" after defeating Istiklol 1-0.[52]
^"Без единой потери очков!". fc-istiklol.tj/ (in Russian). FC Istiklol. 23 November 2020. Archived from the original on 24 October 2022. Retrieved 30 November 2020.