All times given as local time (UTC+2)
Libyan Cup 2008–09: 16 sides from the 16 matches being played in this round will go through to the Round of 32, where they will be joined by the 16 Libyan Premier League teams.
Eastern Section edit
This group will contain 18 sides, 7 of which had qualified from groups A & B in the first round. Over the 9 matches, nine will qualify for the Round of 32.
| Al Taw'eah | 0 – 5 | Shabab al Jabal |
|---|---|---|
Referee: Rafa' Zayed
| Al Baranes | 1 – 1 (5 – 4 pen.) | Shamal Benghazi |
|---|---|---|
| Al Anwaar | 2 – 1 | Al Ansaar |
|---|---|---|
Referee: Ahmed al Jroushi
| Al Mukhtar Tobruk | 1 – 1 (4 – 3 pen.) | Benghazi al Jadeeda |
|---|---|---|
 1H' |
2H' (pen.) |
Referee: Abdallah Fdhail
| Darnes | 1 – 0 | Al Sawaed |
|---|---|---|
Referee: Anwar Abdesalam
| Al Wahda B. | 2 – 0 | Al Najma |
|---|---|---|
| Wefaq Ajdabiya | 1 – 3 | Al Tahaddi |
|---|---|---|
| 2H' |
 Mousa Malik 18' 30'Osama al Qataani  40' 2H' |
Referee: Mohammad al Shelmani
| Al Hilal T. | 1 – 1 (5 – 4 pen.) | Al Hurriya |
|---|---|---|
Referee: Al Taher Fraj
| Nojom Ajdabiya | 2 – 0 | Al Andalus |
|---|---|---|
Referee: Mohammad al Jilaly
Western Section edit
This group will contain 14 sides, 6 of which had qualified from Groups C & D in the first round. Over the 7 ties, 7 teams will go through to the Round of 32.
| Al Hiyad | 0 – 1 | Abi al Ashar |
|---|---|---|
| 89' |
| Al Dhahra Tripoli | 1 – 1 (4 - 3 pens) | Al Mahalla |
|---|---|---|
