The 2008–09 Macedonian Cup is the 17th season of Macedonia's football knockout competition. FK Rabotnički are the defending champions, having won their first title the previous year.
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The draw was held on June 21, 2008 in Skopje. Matches were played on September 17, 2008.
| Team 1 | Score | Team 2 |
|---|---|---|
| Fortuna | 2–3 | Pobeda |
| Ohrid 2004 | 3–0 (f) | Baškimi |
| Bregalnica Štip | (f) 0–3 | Horizont Turnovo |
| Vardino | 0–4 | Milano |
| Karaorman | (f) 0–3 | Belasica |
| Gostivar | (f) 0–3 | Miravci |
| Teteks | 0–1 | Makedonija |
| Lokomotiva | 0–2 | Rabotnički |
| Nov Milenium | 1–0 | Cementarnica |
| Kravari | 0–4 | Škendija 79 |
| Babuna | 0–3 | Vardar |
| Sloga Jugomagnat | 2–4 | Renova |
| 11 Oktomvri | 0–1 | Metalurg |
| Vlazrimi | 0–2 | Sileks |
| Kožuv | 1–4 | Pelister |
| Drita | 2–1 | Napredok |
The draw was held on September 22, 2008 in Skopje. The first legs were played on October 22, 2008 and second on October 29 and 30, 2008.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Metalurg | 0–1 | Milano | 0–1 | 0–0 |
| Vardar | 1–3 | Renova | 1–1 | 0–2 |
| Rabotnički | 3–0 | Nov Milenium | 1–0 | 2–0 |
| Drita | 1–5 | Miravci | 1–1 | 0–4 |
| Sileks | 2–0 | Belasica | 2–0 | 0–0 |
| Pelister | 6–1 | Horizont Turnovo | 4–0 | 2–1 |
| Pobeda | 1–5 | Makedonija | 1–1 | 0–4 |
| Škendija 79 | 5–1 | Ohrid 2004 | 3–0 | 2–1 |
The draw was held on November 6, 2008 in Skopje. The first legs were played on November 26, 2008 and the second were played on December 6 and 10, 2008.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Renova | 0–1 | Rabotnički | 0–0 | 0–1 |
| Sileks | 1–4 | Milano | 0–2 | 1–2 |
| Pelister | 3–4 | Škendija 79 | 3–1 | 0–3 |
| Miravci | 1–4 | Makedonija | 1–1 | 0–3 |
The draw was held on December 25, 2008 in Skopje. The first legs were played on April 8, 2009 and the second were played on May 6, 2009.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Rabotnički | 3–2 | Škendija 79 | 3–1 | 0–1 |
| Makedonija | 2–1 | Milano | 2–0 | 0–1 |
| 24 May 2009 16:30 CEST |
Rabotnički | 1 – 1 | Makedonija | Gradski Stadion, Skopje Referee: Dimitar Mečkarovski |
|---|---|---|---|---|
| Pandev 89' | Klečkarovski 64' | |||
| Penalties | ||||
| Wandeir Filho Trajčev Dimovski Perendija Savić Pandev |
6–5 | de Brito Brnjarčevski Klečkarovski Ilievski Milevski Lena Jovanovski |
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