| Season | League | Cup | Europe | Top goalscorer1 | Notes |
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| Division | P | W | D | L | F | A | Pts | Pos | Name | Goals |
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| 1994–95[47] | First League of Bosnia and Herzegovina Jablanica Group | 5 | 5 | 0 | 0 | 18 | 1 | 15 | 1st | QF | | Elvir Baljić | 8 | 8 |
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First League of Bosnia and Herzegovina Final Play-off | 3 | 1 | 1 | 1 | 3 | 4 | 4 | 2nd |
| 1995–96[48] | First League of Bosnia and Herzegovina | 30 | 12 | 7 | 11 | 38 | 29 | 43 | 7th | SF | | Reuf Herco | 9 | |
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| 1996–97[49] | First League of Bosnia and Herzegovina | 30 | 16 | 8 | 6 | 57 | 23 | 56 | 2nd | Winners | | Smječanin,Uščuplić | 12 | |
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| 1997–98[50] | First League of Bosnia and Herzegovina Bosniaks First League | 30 | 15 | 8 | 7 | 56 | 33 | 53 | 3rd | Winners | | Alen Avdić | 14 | 9 |
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First League of Bosnia and Herzegovina Final Play-off | 3 | 1 | 1 | 1 | 1 | 2 | 4 | 2nd |
| 1998–99[51] | First League of Bosnia and Herzegovina | 30 | 22 | 2 | 6 | 55 | 21 | 68 | 1st | Runners-up | UEFA Cup –Q | Džemo Smječanin | 14 | |
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| 1999–2000[52] | First League of Bosnia and Herzegovina Bosniaks First League | 30 | 16 | 7 | 7 | 54 | 24 | 55 | 3rd | QF | | Almedin Hota | 9 | |
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First League of Bosnia and Herzegovina Final Play-off | 6 | 4 | 0 | 2 | 14 | 6 | 12 | 3rd |
| 2000–01[53] | Premier League of Bosnia and Herzegovina | 42 | 24 | 9 | 9 | 81 | 35 | 81 | 3rd | Runners-up | | Edin Šaranović | 20 | 10 |
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| 2001–02[54] | Premier League of Bosnia and Herzegovina | 30 | 13 | 8 | 9 | 50 | 34 | 47 | 4th | Winners | UEFA Cup –Q | Edin Šaranović | 12 | 11 |
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| Current format ofPremier League of Bosnia and Herzegovina |
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| 2002–03[55] | Premier League of Bosnia and Herzegovina | 30 | 19 | 7 | 12 | 83 | 39 | 69 | 3rd | SF | UEFA Cup –R1 | Emir Obuća | 27 | |
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| 2003–04[56] | Premier League of Bosnia and Herzegovina | 30 | 17 | 5 | 8 | 58 | 25 | 56 | 3rd | QF | UEFA Cup –Q | Alen Škoro | 20 | |
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| 2004–05[57] | Premier League of Bosnia and Herzegovina | 30 | 13 | 6 | 11 | 39 | 37 | 45 | 4th | Winners | | Emir Obuća | 12 | |
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| 2005–06[58] | Premier League of Bosnia and Herzegovina | 30 | 18 | 6 | 6 | 57 | 26 | 60 | 2nd | QF | | Alen Avdić | 13 | |
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| 2006–07[59] | Premier League of Bosnia and Herzegovina | 30 | 17 | 6 | 7 | 44 | 26 | 57 | 1st | SF | | Emir Obuća | 13 | |
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| 2007–08[60] | Premier League of Bosnia and Herzegovina | 30 | 14 | 6 | 10 | 40 | 30 | 48 | 5th | QF | UEFA Champions League –QR3 | Haris Handžić | 9 | |
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| 2008–09[61] | Premier League of Bosnia and Herzegovina | 30 | 14 | 7 | 9 | 43 | 30 | 49 | 4th | R1 | | Admir Raščić | 9 | |
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| 2009–10[62] | Premier League of Bosnia and Herzegovina | 30 | 14 | 8 | 8 | 43 | 25 | 50 | 5th | R2 | UEFA Europa League –QR4 | Alen Škoro | 13 | |
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| 2010–11[63] | Premier League of Bosnia and Herzegovina | 30 | 17 | 6 | 7 | 51 | 26 | 57 | 2nd | QF | | Emir Obuća | 8 | |
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| 2011–12[64] | Premier League of Bosnia and Herzegovina | 30 | 16 | 6 | 8 | 48 | 31 | 54 | 4th | QF | UEFA Europa League –QR3 | Nermin Haskić | 11 | |
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| 2012–13[65] | Premier League of Bosnia and Herzegovina | 30 | 17 | 9 | 4 | 52 | 19 | 60 | 2nd | R2 | UEFA Europa League –QR3 | Emir Hadžić | 26 | |
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| 2013–14[66] | Premier League of Bosnia and Herzegovina | 30 | 17 | 8 | 5 | 66 | 23 | 58 | 3rd | Winners | UEFA Europa League –QR2 | Nikola Komazec | 14 | |
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| 2014–15[67] | Premier League of Bosnia and Herzegovina | 30 | 19 | 9 | 2 | 55 | 17 | 66 | 1st | QF | UEFA Europa League –QR4 | Krste Velkoski | 13 | |
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| 2015–16[68] | Premier League of Bosnia and Herzegovina | 30 | 18 | 3 | 9 | 56 | 28 | 57 | 4th | QF | UEFA Champions League –QR2 | Leon Benko | 18 | |
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| 2016–17[69] | Premier League of Bosnia and Herzegovina | 32 | 16 | 11 | 5 | 41 | 22 | 59 | 3rd | Runners-up | | Mersudin Ahmetović | 12 | 12 |
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| 2017–18[70] | Premier League of Bosnia and Herzegovina | 32 | 17 | 5 | 10 | 58 | 28 | 56 | 3rd | R1 | UEFA Europa League –QR1 | Mersudin Ahmetović | 19 | |
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| 2018–19[71] | Premier League of Bosnia and Herzegovina | 33 | 21 | 7 | 5 | 68 | 20 | 70 | 1st | Winners | UEFA Europa League –QR2 | Mersudin Ahmetović | 16 | 13 |
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| 2019–20[72] | Premier League of Bosnia and Herzegovina | 22 | 13 | 6 | 3 | 38 | 19 | 45 | 1st | R2 | UEFA Champions League –QR1 UEFA Europa League –QR3 | Mersudin Ahmetović | 13 | 14 |
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| 2020–21[73] | Premier League of Bosnia and Herzegovina | 33 | 18 | 11 | 4 | 53 | 24 | 65 | 2nd | Winners | UEFA Champions League –QR2 UEFA Europa League –QR4 | Benjamin Tatar Matthias Fanimo | 13 | |
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| 2021–22[74] | Premier League of Bosnia and Herzegovina | 33 | 13 | 7 | 13 | 37 | 33 | 46 | 4th | Runners-up | UEFA Europa Conference League –QR1 | Dal Varešanović Hamza Čataković Asmir Suljić | 5 | |
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| 2022–23[75] | Premier League of Bosnia and Herzegovina | 33 | 15 | 7 | 11 | 50 | 46 | 52 | 4th | R1 | | Renan Oliveira | 9 | |
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| 2023–24[76] | Premier League of Bosnia and Herzegovina | 33 | 16 | 8 | 9 | 57 | 38 | 5315 | 4th | QF | UEFA Europa Conference League –QR1 | Hamza Čataković | 19 | |
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| 2024–25[77] | Premier League of Bosnia and Herzegovina | 33 | 18 | 11 | 4 | 59 | 24 | 65 | 3rd | Winners | UEFA Conference League –QR2 | Giorgi Guliashvili | 21 | |
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