Europa League 2020/21, Third qualifying round |
 | 24.09.2020 |  | Shkëndija | – | Tottenham Hotspur |  | 1:3 (0:1) * |
| Skopje |
Europa League 2020/21, Second qualifying round |
| 17.09.2020 |  | Botoșani | – | Shkëndija | | 0:1 (0:1) * |
| Botoşani |
Europa League 2020/21, First Qualifying Round |
| 27.08.2020 |  | Sumqayıt | – | Shkëndija | | 0:2 (0:0) * |
| Sumqayıt |
Europa League 2019/20, Second qualifying round |
| 30.07.2019 |  | F91 | – | Shkëndija | | 1:1 (0:0) |
| Lëtzebuerg |
Europa League 2019/20, Second qualifying round |
| 23.07.2019 | | Shkëndija | – | F91 | | 1:2 (1:0) |
| Skopje |
Europa League 2018/19, Play-off Round |
| 30.08.2018 | | Shkëndija | – | Rosenborg |  | 0:2 (0:0) |
| Skopje |
Europa League 2018/19, Play-off Round |
| 23.08.2018 | | Rosenborg | – | Shkëndija | | 3:1 (3:0) |
| Trondheim |
Europa League 2017/18, Play-off Round |
| 24.08.2017 | | Shkëndija | – | Milan |  | 0:1 (0:1) |
| Skopje |
Europa League 2017/18, Play-off Round |
| 17.08.2017 | | Milan | – | Shkëndija | | 6:0 (3:0) |
| Milano |
Europa League 2017/18, Third qualifying round |
| 03.08.2017 | | Shkëndija | – | Trakai |  | 3:0 (2:0) |
| Strumica |
Europa League 2017/18, Third qualifying round |
| 27.07.2017 | | Trakai | – | Shkëndija | | 2:1 (1:1) |
| Vilnius |
Europa League 2017/18, Second qualifying round |
| 20.07.2017 |  | HJK | – | Shkëndija | | 1:1 (1:0) |
| Helsinki |
Europa League 2017/18, Second qualifying round |
| 13.07.2017 | | Shkëndija | – | HJK | | 3:1 (1:1) |
| Strumica |
Europa League 2017/18, First Qualifying Round |
| 06.07.2017 |  | Dacia | – | Shkëndija | | 0:4 (0:2) |
| Speia |
Europa League 2017/18, First Qualifying Round |
| 29.06.2017 | | Shkëndija | – | Dacia | | 3:0 (2:0) |
| Strumica |
Europa League 2016/17, Play-off Round |
| 25.08.2016 | | Shkëndija | – | Gent |  | 0:4 (0:0) |
| Skopje |
Europa League 2016/17, Play-off Round |
| 18.08.2016 | | Gent | – | Shkëndija | | 2:1 (1:1) |
| Gent |
Europa League 2016/17, Third qualifying round |
| 04.08.2016 |  | Mladá Boleslav | – | Shkëndija | | 1:0 (0:0) |
| Mladá Boleslav |
Europa League 2016/17, Third qualifying round |
| 28.07.2016 | | Shkëndija | – | Mladá Boleslav | | 2:0 (0:0) |
| Skopje |
Europa League 2016/17, Second qualifying round |
| 21.07.2016 | | Shkëndija | – | Neftçi | | 1:0 (1:0) |
| Skopje |
Europa League 2016/17, Second qualifying round |
| 14.07.2016 | | Neftçi | – | Shkëndija | | 0:0 |
| Bakı |
Europa League 2016/17, First Qualifying Round |
| 07.07.2016 |  | Cracovia | – | Shkëndija | | 1:2 (0:1) |
| Kraków |
Europa League 2016/17, First Qualifying Round |
| 30.06.2016 | | Shkëndija | – | Cracovia | | 2:0 (1:0) |
| Skopje |
Europa League 2015/16, First Qualifying Round |
| 09.07.2015 |  | Aberdeen | – | Shkëndija | | 0:0 |
| Aberdeen |
Europa League 2015/16, First Qualifying Round |
| 02.07.2015 | | Shkëndija | – | Aberdeen | | 1:1 (0:0) |
| Skopje |
Europa League 2014/15, First Qualifying Round |
| 10.07.2014 | | Zimbru | – | Shkëndija | | 2:0 (1:0) |
| Chişinău |
Europa League 2014/15, First Qualifying Round |
| 01.07.2014 | | Shkëndija | – | Zimbru | | 2:1 (1:0) |
| Skopje |
Europa League 2012/13, First Qualifying Round |
| 10.07.2012 |  | Portadown | – | Shkëndija | | 2:1 (0:1) |
| Portadown |
Europa League 2012/13, First Qualifying Round |
| 03.07.2012 | | Shkëndija | – | Portadown | | 0:0 |
| Tetovo |
