| 1. Round | 10/09/2016 | Atalanta [Youth] | - | Frosinone Calcio [Youth] | 3:2 | ||||
| 2. Round | 17/09/2016 | FC Crotone [Youth] | - | Atalanta [Youth] | 2:3 | ||||
| 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 |  |
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| 6. Round | 22/10/2016 | Atalanta [Youth] | - | Bologna FC [Youth] | 4:2 | |
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| 8. Round | 19/11/2016 | Atalanta [Youth] | - | Ternana Calcio [Youth] | 5:0 |  |
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| 11. Round | 10/12/2016 | Pisa SC [Youth] | - | Atalanta [Youth] | 1:1 | ||||
| 12. Round | 17/12/2016 | Atalanta [Youth] | - | AS Roma [Youth] | 1:0 | ||||
| 18. Round | 18/02/2017 | Atalanta [Youth] | - | Genoa CFC [Youth] | 5:1 | |
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| 20. Round | 04/03/2017 | Atalanta [Youth] | - | Cagliari Calcio [Youth] | 3:0 | |
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| 22. Round | 01/04/2017 | Atalanta [Youth] | - | Virtus Entella [Youth] | 2:2 |
Italy