The 2003–04 Maltese FA Trophy was the 66th season since its establishment. The competition started on 1 November 2003 and ended on 18 May 2004 with the final, which Sliema Wanderers won 2-0 against Marsaxlokk.[1]
| Team 1 | Score | Team 2 |
|---|---|---|
| 1 November 2003 | ||
| Marsaxlokk | 1–0 | St. Patrick |
| San Gwann | 2–3 (a.e.t.) | Msida St. Joseph |
| 8 November 2003 | ||
| Hamrun Spartans | 3–0 | Marsa |
| Pietà Hotspurs | 2–0 | Senglea Athletic |
| 15 November 2003 | ||
| Mosta | 4–1 | Naxxar Lions |
| Lija Athletic | 2–0 | Mqabba |
| 22 November 2003 | ||
| Rabat Ajax | 1–3 | Balzan Youths |
| Tarxien Rainbows | 0–1 | Floriana |
| Team 1 | Score | Team 2 |
|---|---|---|
| 21 February 2004 | ||
| Floriana | 1–0 | Balzan Youths |
| Pietà Hotspurs | 1–3 | Marsaxlokk |
| 22 February 2004 | ||
| Mosta | 3–1 | Lija Athletic |
| 1 March 2004 | ||
| Msida St. Joseph | 2–1 | Hamrun Spartans |
| Team 1 | Score | Team 2 |
|---|---|---|
| 3 April 2004 | ||
| Msida St. Joseph | 0–1 | Sliema Wanderers |
| Valletta | 1–0 | Floriana |
| 4 April 2004 | ||
| Mosta | 0–5 | Birkirkara |
| Hibernians | 1–4 | Marsaxlokk |
| 12 May 2004 | Marsaxlokk | 1–0 (a.e.t.) | Valletta | Ta' Qali |
Bogdanović  115' |
Report | Stadium: Ta' Qali National Stadium Referee: Chris Lautier |
| 13 May 2004 | Sliema Wanderers | 2–1 | Birkirkara | Ta' Qali |
| Giglio 29' Mifsud 68' |
Report | Dronca 76' (pen.) |
Stadium: Ta' Qali National Stadium Referee: Joe Attard |
| Marsaxlokk | 0–2 | Sliema Wanderers |
|---|---|---|
| Report | Brincat 29' Giglio 86' |
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| Domestic cups |
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| Lists |
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