A record number of 67 clubs competed in the FA Trophy, with the first round starting on the weekend of 1–2 September 2018 and concluding with the final played on 18 May 2019.

[1] Valletta were the defending champions, but lost in the final to Balzan on penalties, the latter winning their first ever FA Trophy title.

Matches which are level after regulation advanced to extra time and afterwards to penalties to determine a winner, when needed.

The top six position from 2017-18 Maltese Premier League teams that are seeded in the third round of the FA Trophy.

On 23 February 2019, four quarter-final matches were postponed amid safety concerns caused by the inclement weather, warnings of gale-force winds and hail-storm.

[4] The first FA Trophy quarter-final match between Pietà Hotspurs and Gżira United, at the Hibernians Stadium, was abandoned by referee Emanuel Grech in the 88th minute, and finished on 3 May 2019 at Ta' Qali National Stadium, 19:00, from the point of abandonment.