| 1. Round | 10/09/2016 | Atalanta [Youth] | - | Frosinone Calcio [Youth] | 3:2 | ||||
| 3. Round | 23/09/2016 | US Palermo [Youth] | - | Atalanta [Youth] | 1:1 | ||||
| 4. Round | 01/10/2016 | Atalanta [Youth] | - | Novara Calcio [Youth] | 3:0 | ||||
| 5. Round | 15/10/2016 | Genoa CFC [Youth] | - | Atalanta [Youth] | 2:4 | ||||
| 6. Round | 22/10/2016 | Atalanta [Youth] | - | Bologna FC [Youth] | 4:2 | ||||
| 7. Round | 05/11/2016 | Cagliari Calcio [Youth] | - | Atalanta [Youth] | 0:1 | ||||
| 9. Round | 26/11/2016 | Virtus Entella [Youth] | - | Atalanta [Youth] | 3:1 |  |
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| 10. Round | 03/12/2016 | Atalanta [Youth] | - | Inter [Youth] | 1:2 | ||||
| 14. Round | 21/01/2017 | Frosinone Calcio [Youth] | - | Atalanta [Youth] | 2:1 | |
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| 15. Round | 28/01/2017 | Atalanta [Youth] | - | FC Crotone [Youth] | 3:0 | ||||
| 23. Round | 08/04/2017 | Inter [Youth] | - | Atalanta [Youth] | 1:3 | ||||
| 24. Round | 15/04/2017 | Atalanta [Youth] | - | Pisa SC [Youth] | 5:0 | ||||
| 25. Round | 29/04/2017 | AS Roma [Youth] | - | Atalanta [Youth] | 0:3 |
Italy