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| Saturday 24th September 2016 | |||
| Group F – U 15 | Mellieha | 1 – 0 | Qormi |
| Sec D – U 15 | Ghaxaq | 0 – 4 | Sirens |
| Sec E – U 17 | Sta. Venera | 0 – 2 | Mtarfa |
| Group D – U 15 | Zabbar | 1 – 7 | Melita |
| Group C – U 17 | Hamrun | 2 – 1 | Rabat |
| Sec D – U 15 | Fgura | 0 – 4 | Rabat |
| Group A – U 15 | Luqa | 0 – 5 | Valletta |
| Group B – U 15 | Marsa | 0 – 2 w/o | Paola Hibs |
| Sunday 25th September 2016 | ||||
| Group A – U 17 | St. Andrews | 7 – 0 | Zabbar | |
| Group H – U 15 | Naxxar | 0 – 3 | St. Andrews | |
| Group F – U 17 | Pieta | 1 – 0 | Pembroke | |
| Group B – U 17 | Mosta | 4 – 0 | Tarxien | |
| Group C – U 15 | Gozo | 0 – 1 | Mosta | |
| Group E – U 17 | Floriana | 3 – 1 | Zejtun | |
| Sec D – U 15 | Zejtun | 3 – 3 | Attard | |
| Group H – U 17 | Balzan | 3 – 0 | Lija/Iklin | |
| Group G – U 15 | Lija/Iklin | 1 – 4 | Birkirkara | |
| Group D – U 17 | Birkirkara | 7 – 0 | Swieqi | |
| Sec D – U 15 | Zebbug | Posp. | Mqabba | |
| Group G – U 17 | Sliema | Posp. | Mqabba | |
| Sec E – U 17 | Gzira | Posp. | Kalkara | |