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The 2008–09 Croatian Football Cup was the eighteenth season of Croatia's football knockout competition. Dinamo Zagreb were the defending champions since they won the last year's cup by defeating Hajduk Split 3–0 on aggregate.

Calendar

Round	Main date	Number of fixtures	Clubs	New entries this round
Preliminary round	27 August 2008	16	48 → 32	none
First round	23 and 24 September 2008	16	32 → 16	16
Second round	29 October 2008	8	16 → 8	none
Quarter-finals	12 and 26 November 2008	8	8 → 4	none
Semi-finals	4 and 18 March 2009	4	4 → 2	none
Final	13 and 28 May 2009	2	2 → 1	none

The preliminary round was held on 27 August 2008.

Tie no	Home team	Score	Away team
1	Žminj	0–2	Gaj Mače
2	Moslavina	7–0	Istra Tar
3	Croatia Đakovo	1–3	Polet Buševec
4	Bjelovar	2–4	Zagora Unešić
5	Orijent	1–0	Raštane
6	Novalja	0–1	Metalac Sisak
7	Međimurje	3–0	Trogir
8	Suhopolje	1–1 (5–4 p)	Križevci
9	Mladost Cernik	2–0	Slavija Pleternica
10	Vukovar '91	3–2	Podravina
11	Nedelišće	1–3	Karlovac
12	Garić Garešnica	1–4	Grafičar Vodovod
13	Mladost Molve	3–4 (aet)	Konavljanin
14	Hrvatski Dragovoljac	1–0	Graničar
15	Lučko	11–1	Sračinec
16	Vinogradar	1–2	Oriolik

The matches were played on 23 and 24 September 2008.

Tie no	Home team	Score	Away team
1	Gaj Mače	1–5	Dinamo Zagreb
2	Metalac Sisak	0–6	Rijeka
3	Orijent	1–4	Hajduk Split
4	Mladost Cernik	0–1	Varteks
5	Polet Buševec	0–2	Slaven Belupo
6	Zagora Unešić	2–1	Osijek
7	Grafičar Vodovod	1–3	NK Zagreb
8	Suhopolje	1–2	Cibalia
9	Oriolik	w/o¹	Kamen Ingrad
10	Lučko	3–5	Inter Zaprešić
11	Karlovac	1–1 (7–6 p)	Istra 1961
12	Moslavina	2–1	Šibenik
13	Vukovar '91	0–1	Pomorac
14	Konavljanin	1–0	Belišće
15	Zadar	3–0	Naftaš HAŠK
16	Hrvatski Dragovoljac	1–0	Međimurje

¹Due to financial difficulties, Kamen Ingrad ceased competing on a senior professional level, and therefore withdrew from the competition.

The matches were played on 29 October 2008.

Tie no	Home team	Score	Away team
1	Hrvatski Dragovoljac	0–6	Dinamo Zagreb
2	Zadar	2–2 (6–7 p)	Rijeka
3	Konavljanin	0–2	Hajduk Split
4	Pomorac	2–0	Varteks
5	Moslavina	0–2	Slaven Belupo
6	Zagora Unešić	2–1	Karlovac
7	Inter Zaprešić	0–2	NK Zagreb
8	Oriolik	0–4	Cibalia

The draw was held on 30 October. First legs were held on 12 November and second legs on 26 November 2008.

Team 1	Agg.Tooltip Aggregate score	Team 2	1st leg	2nd leg
Rijeka	4–4 (2–4 p)	NK Zagreb	2–2	2–2 (aet)
Pomorac	2–2 (2–4 p)	Cibalia	1–1	1–1 (aet)
Hajduk Split	0–0 (7–6 p)	Slaven Belupo	0–0	0–0 (aet)
Zagora Unešić	2–7	Dinamo Zagreb	1–2	1–5