In this page the junior champions from 1987 onwards are listed. Actually the first Malta Junior Championship was held in 1946. Currently the Malta Chess Federation is doing all its best to try to find out and build a complete list of champions from 1946 onwards.
| Year | Champions |
| 1987 | Duncan Vella |
| 1988 | Joseph Stafrace |
| 1989 | Joseph Stafrace |
| 1990 | Joseph Stafrace |
| 1991 | Duncan Vella |
| 1992 | Timothy Mifsud |
| 1993 | Timothy Mifsud |
| 1994 | Timothy Mifsud |
| 1995 | Peter Pullicino |
| 1996 | David Cilia Vincenti |
| 1997 | Colin Pace |
| 1998 | Timothy Mifsud |
| 1999 | Colin Pace |
| 2000 | Daniel Abela |
| 2001 | Daniel Abela |
| 2002 | Daniel Abela |
| 2003 | Charles Sinn |