| ROUND | Q1 | Q2 | Q3 | Q4 | R1 | R2 | R3 | QF | SF | F | |||||||||||||
| l1 | l2 | l1 | l2 | l1 | l2 | l1 | l2 | r1 | r2 | r3 | r4 | r5 | r6 | l1 | l2 | l1 | l2 | l1 | l2 | l1 | l2 | ||
| Season archive |
| Thursday, 28 July 2016 | ||||||
| q3l1 |  Lille | 1-1 | Qabala | |||
| q3l1 |  AA Gent | 5-0 | Farul Constanța | |||
| q3l1 |  IFK Göteborg | 1-2 | HJK | |||
| q3l1 |  Aberdeen | 1-1 | Maribor | |||
| q3l1 |  AZ | 1-0 | PAS Giannina | |||
| q3l1 | Heracles Almelo | 1-1 | Arouca | |||
| q3l1 | Saint-Étienne | 0-0 | AEK | |||
| q3l1 | Panathinaikos | 1-0 | AIK | |||
| q3l1 |  Grasshoppers | 2-1 | Apollon | |||
| q3l1 |  FK Austria | 0-1 | Spartak Trnava | |||
| q3l1 |  MOL Fehérvár | 0-1 | FC Midtjylland | |||
| q3l1 |  Slavia Praha | 0-0 | Rio Ave | |||
| q3l1 | Luzern | 1-1 | Sassuolo | |||
| q3l1 |  Hertha BSC Berlin | 1-0 | Brøndby | |||
| q3l1 | Racing Genk | 1-0 | Cork City | |||
| q3l1 |  Vojvodina | 1-1 | Dinamo Minsk | |||
| q3l1 |  Zagłębie Lubin | 1-2 | SønderjyskE | |||
| q3l1 | AEK | 1-1 | Spartak | |||
| q3l1 |  Birkirkara | 0-3 | FK Krasnodar | |||
| q3l1 | Domžale | 2-1 | West Ham United | |||
| q3l1 |  Ankaraspor | 1-0 | Nõmme Kalju | |||
| q3l1 | Torpedo Zhodino | 0-0 | SK Rapid Wien | |||
| q3l1 | İstanbul Başakşehir | 0-0 | Rijeka | |||
| q3l1 | Admira | 1-2 | Slovan Liberec | |||
| q3l1 | Pandurii | 1-3 | Maccabi Tel Aviv | |||
| q3l1 |  Shkëndija | 2-0 | Mladá Boleslav | |||
| q3l1 | Lokomotiva | 0-0 | Vorskla-Naftohaz | |||
| q3l1 | PFK Oleksandriya | 0-3 | Hajduk Split | |||
| q3l1 |  Jelgava* | 1-1 | Beitar Jerusalem | |||
| Wednesday, 3 August 2016 | ||||||
| q3l2 | Slovan Liberec | 2-0 | Admira | 4-1 | ||
| Thursday, 4 August 2016 | ||||||
| q3l2 | West Ham United | 3-0 | Domžale | 4-2 | ||
| q3l2 | Brøndby | 3-1 | Hertha BSC Berlin | 3-2 | ||
| q3l2 | Spartak | 0-1 | AEK | 1-2 | ||
| q3l2 | AEK | 0-1 | Saint-Étienne | 0-1 | ||
| q3l2 | HJK | 0-2 | IFK Göteborg | 2-3 | ||
| q3l2 | AIK | 0-2 | Panathinaikos | 0-3 | ||
| q3l2 | Hajduk Split | 3-1 | PFK Oleksandriya | 6-1 | ||
| q3l2 | Cork City | 1-2 | Racing Genk | 1-3 | ||
| q3l2 | Rijeka | 2-2 | İstanbul Başakşehir | 2-2 | ||
| q3l2 | SK Rapid Wien | 3-0 | Torpedo Zhodino | 3-0 | ||
| q3l2 | Maccabi Tel Aviv | 2-1 | Pandurii | 5-2 | ||
| q3l2 | Dinamo Minsk | 0-2 | Vojvodina | 1-3 | ||
| q3l2 | Rio Ave | 1-1 | Slavia Praha | 1-1 | ||
| q3l2 | Beitar Jerusalem | 3-0 | Jelgava* | 4-1 | ||
| q3l2 | Maribor | 1-0 | Aberdeen | 2-1 | ||
| q3l2 | Spartak Trnava | 0-1 | FK Austria | 1-1, aet, p4-5 | ||
| q3l2 | Sassuolo | 3-0 | Luzern | 4-1 | ||
| q3l2 | Vorskla-Naftohaz | 2-3 | Lokomotiva | 2-3 | ||
| q3l2 | Apollon | 3-3 | Grasshoppers | 4-5, aet | ||
| q3l2 | FC Midtjylland | 1-1 | MOL Fehérvár | 2-1, aet | ||
| q3l2 | SønderjyskE | 1-1 | Zagłębie Lubin | 3-2 | ||
| q3l2 | Mladá Boleslav | 1-0 | Shkëndija | 1-2 | ||
| q3l2 | PAS Giannina | 1-2 | AZ | 1-3 | ||
| q3l2 | Nõmme Kalju | 0-2 | Ankaraspor | 0-3 | ||
| q3l2 | Qabala | 1-0 | Lille | 2-1 | ||
| q3l2 | FK Krasnodar | 3-1 | Birkirkara | 6-1 | ||
| q3l2 | Arouca | 0-0 | Heracles Almelo | 1-1 | ||
| q3l2 | Farul Constanța | 0-0 | AA Gent | 0-5 | ||
