Floriana were paired with Hamrun Spartans, Balzan with Tarxien Rainbows while SK Victoria Wanderers will be hosting Pembroke Athleta.
The quarter-finals are scheduled for February 18 and 19.
Sliema Wanderers defeated Mosta 3-2 and Qrendi 5-0 in the previous rounds. Senglea beat Gozitans Xaghra United 7-1 in the second round, Hibernians 3-2 after extra-time in the third round and Vittoriosa Stars 2-1 after extra-time in the fourth round.
Floriana beat Second Division side Birzebbuga St. Peter’s 5-0 and Gozitan champions Ghajnsielem 4-1 in the previous rounds. The Spartans defeated Nadur Youngsters 2-0 and Mqabba 1-0.
Balzan beat Zebbug Rangers 3-1 and Valletta 1-0 in the previous rounds while Tarxien defeated First Division sides Gharghur and Lija Athletic 6-0 and 3-0 respectively.
SK Victoria Wanderers defeated St. Venera Lightnings 3-0, Melita 2-1, Mgarr United 5-0 and St. Andrews 1-0. Pembroke beat Sirens and Marsa with identical 2-1 scores.
FA TROPHY QUARTER-FINALS
Balzan vs Tarxien Rainbows
SK Victoria Wanderers vs Pembroke Athleta
Floriana vs Hamrun Spartans
Senglea Athletic vs Sliema Wanderers