The FC Istiklol 2025 season was Istiklol's seventeenth Tajik League season, of which they were defending Tajik League Champions, and also participated in the Tajik Cup, Tajik Supercup and AFC Champions League Two.
On 14 January, Istiklol announced that their contracts with Darko Ilieski, Dimitar Mitkov and Francesco Margiotta had all ended and the players had left the club.
On 16 January, Istiklol announced that Shervoni Mabatshoev had left the club to sign a 18-month contract with Kapaz.
On 22 January, Istiklol announced the signing of Masrur Gafurov from Barkchi Hisor to a three-year contract.
On 23 January, Istiklol announced the signing of Joseph Okoro from Dinamo Minsk to a one-year contract.
On 24 January, Istiklol announced the signing of Mukhammadzhon Rakhimov from Ravshan Kulob.
On 28 January, Istiklol announced the return of Dà ¾enis BeganoviÃÂ, on a one-year contract.
On 14 February, Istiklol announced the signing of Reza Dehghani, who'd last played for Mes Rafsanjan, to a one-year contract.
On 16 February, Istiklol announced the signing of Lawrence Nicholas, who'd last played for Fatih Karagümrük, to a one-year contract.
On 17 February, Istiklol announced that Khaydar Sattorov had joined Hulbuk and that Mekhron Madaminov had joined Barkchi Hisor, both on loan for the season.
On 19 February, Istiklol announced that Romish Jalilov and Shahrom Sulaymonov had both re-signed for the club after spending the previous season at Khosilot Farkhor.
On 20 February, Istiklol announced that Olimjon Juraev and Shukhratdzhon Shonazarov had joined Sardor on loan for the season. Later on the same day, Istiklol announced that they had extended their contracts with Mukhriddin Khasanov, Tabrezi Davlatmir, Alisher Dzhalilov and Manuchekhr Dzhalilov.
On 24 February, Istiklol announced the signing of Joshua Akpudje, who'd last played for Ilves, to a one-year contract.
On 26 February, Istiklol announced the signing of Muzaffar Safaralii from CSKA Pamir Dushanbe to a three-year contract.
On 10 July, Istiklol announced the return of Manuchekhr Safarov from Dinamo Samarqand.
On 16 July, Istiklol announced the departure of Ruslan Khayloyev, Lawrence Nicholas and Abubakar Umar by mutual consent.
On 19 July, Istiklol announced the departure of Joshua Akpudje by mutual consent.
On 21 July, Istiklol announced the signing of Kirill Suslov from Sochi, to a one-year contract.
On 28 July, Istiklol announced the signing of Siavash Hagh Nazari from Nassaji Mazandaran and the return of Ehson Panjshanbe from Sogdiana, both on contracts until the end of the season. The following day, 29 July, Istiklol announced the signing of Rudolf Turkaj from Suhareka also on a contract until the end of the season.
On 30 July, Istiklol announced the signing of Paul Komolafe from Khujand.
On 31 July, Istiklol announced the signing of Marlen Chobanov from Shurtan.
On 29 December, Istiklol announced that the contracts of Igor Cherevchenko and his coaching staff had expired and that they had left the club.
|- |colspan="16"|Youth team players: |- |colspan="16"|Players away from Istiklol on loan: |- |colspan="16"|Players who left Istiklol during the season: