The Maltese Second and Third Division Knock-Out was a football competition contested by teams playing in the Maltese Second and Third Division. The format consisted of the teams being drawn into eight groups, with the winners of each group progressing to the knockout phase of the competition.
| Match decided by a penalty shoot-out after extra time |
| Season | Winners | Score | Runners–up | |
|---|---|---|---|---|
| 2000–01 | Żebbuġ Rangers | 4–1 | Vittoriosa Stars | |
| 2001–02 | Dingli Swallows | 2–0 | Żebbuġ Rangers | |
| 2002–03 | Tarxien Rainbows | 4–1 | Sirens | |
| 2003–04 | Mellieħa | 2–1 | Żebbuġ Rangers | |
| 2004–05 | Qormi | 1–0 | Mellieħa | |
| 2005–06 | Qormi | 1–0 | Gżira United | |
| 2006–07 | Balzan Youths | 2–0 | Birżebbuġa St. Peter's | |
| 2007–08 | Melita | 5–1 | Balzan Youths | |
| 2008–09 | Melita | 3–0 | St. Venera Lightnings | |
| 2009–10 | Żejtun Corinthians | 2–1 | Għargħur | |
| 2010–11 | Żejtun Corinthians | 2–0 | Rabat Ajax |