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| Saturday 8th October 2016 | |||
| Group B – U 15 | San Gwann | 1 – 0 | Paola Hibs |
| Group E – U 17 | Zejtun | 0 – 8 | Floriana |
| Sec D – U 15 | Zejtun | 4 – 0 | Ghaxaq |
| Group H – U 17 | Lija/Iklin | 1 – 4 | Balzan |
| Group A – U 15 | Balzan | 0 – 4 | Valletta |
| Group D – U 15 | Kirkop | 1 – 2 | Melita |
| Group F – U 15 | Pembroke | 0 – 2 | Qormi |
| Group G – U 17 | Mqabba | 1 – 2 | Sliema |
| Sec E – U 15 | Dingli | 1 – 1 | Swieqi |
| Sunday 9th October 2016 | |||
| Group A – U 17 | Zabbar | 0 – 5 | St. Andrews |
| Group H – U 15 | Sliema | 1 – 5 | St. Andrews |
| Group F – U 17 | Pembroke | 1 – 5 | Pieta |
| Group E – U 15 | Floriana | 0 – 4 | Pieta |
| Group C – U 17 | Rabat | 0 – 3 | Hamrun |
| Group C – U 15 | Hamrun | 1 – 0 | Gozo |
| Group B – U 17 | Tarxien | 2 – 3 | Mosta |
| Group G – U 15 | Tarxien | 2 – 4 | Birkirkara |
| Group D – U 17 | Swieqi | 1 – 9 | Birkirkara |
| Sec E – U 17 | Mtarfa | 1 – 0 | Kalkara |
| Sec D – U 15 | Attard | 4 – 1 | Mqabba |
| Sec E – U 15 | Xghajra | 3 – 0 | Mgarr |
| Sec E – U 17 | Sta. Venera | 1 – 4 | Xghajra |
| Sec E – U 15 | Mtarfa | 3 – 2 | Marsaskala |
| Sec E – U 15 | Marsaxlokk | 1 – 3 | Zurrieq |
| Sec D – U 15 | Fgura | 0 – 4 | Zebbug |