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.
The preliminary round was held on 27 August 2008.
The matches were played on 23 and 24 September 2008.
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.
The draw was held on 30 October. First legs were held on 12 November and second legs on 26 November 2008.
Dinamo Zagreb won 6–1 on aggregate
Hajduk Split won 4–1 on aggregate
3–3 on aggregate. Dinamo Zagreb won 4–3 in penalty shootout.