It featured 20 teams from Maltese Premier League and First Division.
Hibernians received a bye because they won the 2006–07 Maltese FA Trophy.
Other three teams who received a bye directly to the Quarterfinals were Birkirkara, Marsaxlokk and Sliema Wanderers, for being three best-placed teams in previous year's Premier League.
They all finished 2-1 in favour of Valletta, Floriana and Birkirkara who beat Hibernians, Sliema Wanderers and Marsaxlokk respectively.
Michael Galea opened the scoring for Birkirkara but Hamrun Spartans levelled matters through Ryan Fenech but Michael Galea scored his 2nd to give Birkirkara the trophy.