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| Saturday 29th October 2016 | |||
| Sec A – U 17 | Birkirkara | 0 – 0 | San Gwann |
| Sec A – U 15 | Melita | 1 – 3 | Pieta |
| Sec D – U 17 | Naxxar | 2 – 7 | Birzebbugia |
| Sec C – U 15 | Marsa | 0 – 5 | Mellieha |
| Sec C – U 15 | Sliema | 2 – 0 | Gozo |
| Sec D – U 17 | Mgarr | 3 – 0 | Msida |
| Sec E – U 15 | Mgarr | 0 – 2 | Zurrieq |
| Sec B – U 15 | Pembroke | 0 – 2 | Hamrun |
| Sec A – U 17 | Hamrun | 4 – 3 | Balzan |
| Sec B – U 15 | Paola Hibs | 2 – 0 | Balzan |
| Sunday 30th October 2016 | |||
| Sec B – U 17 | Qormi | 2 – 2 | Pembroke |
| Sec A – U 15 | San Gwann | 1 – 0 | Qormi |
| Sec A – U 17 | St. Andrews | 2 – 1 | Mosta |
| Sec A – U 15 | St. Andrews | 5 – 3 | Mosta |
| Sec A – U 17 | Valletta | 1 – 1 | Pieta |
| Sec A – U 15 | Valletta | 3 – 1 | Birkirkara |
| Sec E – U 15 | Dingli | 1 – 5 | Mtarfa |
| Sec E – U 17 | Gzira | 3 – 0 | Kalkara |
| Sec E – U 15 | Marsaskala | 1 – 0 | Xghajra |
| Sec B – U 17 | Melita | 0 – 4 | Sliema |
| Sec E – U 15 | Marsaxlokk | 2 – 4 | Swieqi |
| Sec B – U 17 | Paola Hibs | 3 – 0 | Zebbug |
| Sec C – U 15 | Luqa | 6 – 0 | Tarxien |
| Sec D – U 17 | Mellieha | 2 – 1 | Attard |
| Sec B – U 15 | Kirkop | 3 – 2 | Naxxar |
| Sec B – U 17 | Kirkop | 1 – 0 | Floriana |
| Sec B – U 15 | Floriana | 1 – 0 | Lija/Iklin |