| 2. Round | 10/07/2016 | Atlético Junior | - | Independiente Medellín | 1:1 | ||||
| 8. Round | 13/08/2016 | Atlético Junior | - | Águilas Doradas | 1:1 | ||||
| 9. Round | 21/08/2016 | Deportes Tolima | - | Atlético Junior | 1:1 | ||||
| 10. Round | 28/08/2016 | Atlético Junior | - | Jaguares de Córdoba | 1:0 |  |
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| 7. Round | 04/09/2016 | Jaguares de Córdoba | - | Atlético Junior | 0:0 | ||||
| 1. Round | 08/09/2016 | Atlético Huila | - | Atlético Junior | 3:1 | |
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| 11. Round | 11/09/2016 | Atlético Junior | - | Fortaleza FC | 1:2 | ||||
| 13. Round | 17/09/2016 | Atlético Junior | - | Once Caldas | 0:1 | ||||
| 14. Round | 26/09/2016 | Boyacá Chicó | - | Atlético Junior | 2:2 | ||||
| 3. Round | 08/10/2016 | Patriotas FC | - | Atlético Junior | 3:2 | ||||
| 16. Round | 15/10/2016 | Atlético Bucaramanga | - | Atlético Junior | 3:0 | ||||
| 17. Round | 22/10/2016 | Deportivo Cali | - | Atlético Junior | 2:0 | ||||
| 18. Round | 30/10/2016 | Atlético Junior | - | Envigado FC | 2:1 | |
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| 15. Round | 04/11/2016 | Atlético Junior | - | Millonarios | 2:1 | |
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| 19. Round | 06/11/2016 | Cortuluá | - | Atlético Junior | 1:2 | |
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| 12. Round | 10/11/2016 | Atlético Nacional | - | Atlético Junior | 2:2 | |
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| 20. Round | 20/11/2016 | Atlético Junior | - | La Equidad | 2:1 | |
Colombia