The 2019–20 Maltese FA Trophy was the 82nd edition of the football cup competition.
On 18 May 2020, the Malta FA Executive Committee decided to terminate the competition due to the COVID-19 pandemic.
Matches which are level after regulation advanced to extra time and afterwards to penalties to determine a winner, when needed.
The draws were made on 6 August 2018 and were conducted by Dr. Angelo Chetcuti, the General Secretary of the Malta Football Association, and Rodney Pisani, the Deputy General Secretary of the Association who leads the Competitions Department.
The top six position from 2018-19 Maltese Premier League teams that are seeded in the third round of the FA Trophy.
On 18 May 2020, the Malta FA Executive Committee decided to terminate the competition due to the COVID-19 pandemic.