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The team first appeared in official competitions in the 2005 European Championship's qualifying, debuting on August 10, 2003 in Bucharest with a 3–0 loss to Romania. Malta lost all eight games, scoring once and conceding 35. The team's first goal was scored by Sarah Caruana on November 16, 2003, against Croatia in a match played at the Gozo Stadium.

After 13 losses, Malta achieved its first draw on June 7, 2006 against Bosnia and Herzegovina in the last match of the 2007 World Cup's qualifying. The team played in the 2011 World Cup's qualifying, losing all games including a record 0–13 defeat to Spain. On March 3, 2011 Malta won an official match for the first time in the 2013 European Championship qualifying's preliminary round, beating Georgia 1–0 with a goal by D'Agostino in injury time.

On April 6, 2013 Malta beat Luxembourg 6–0 in the 2015 World Cup qualifying's preliminary round. The team also defeated Latvia and drew with Albania to top the group and make it past a preliminary round for the first time.

The team was coached from its foundation until 2014 by Pierre Brincat, and then from 2015 till 2022 by former U19 coach Mark Gatt. Former Italian international Manuela Tesse was appointed as the head coach as from 1 January 2023