| Croatian Football Cup | |
| Year: | 1999–2000 |
| Country: | Croatia |
| Num Teams: | 48 |
| Defending Champions: | Osijek |
| Winners: | Hajduk Split (3rd title) |
| Second: | Dinamo Zagreb |
| Matches: | 54 |
| Goals: | 178 |
| Scoring Leader: | Robert Prosinečki (5) |
| Prev Season: | 1998–99 |
| Next Season: | 2000–01 |
The 1999–2000 Croatian Football Cup was the ninth edition of Croatia's football knockout competition. Osijek were the defending champions, and it was won by Hajduk Split.
| Round | Main date | Number of fixtures | width=100 | Clubs ! | New entries this round |
|---|---|---|---|---|---|
| 4–15 August 1999 | 16 | 48 → 32 | none | ||
| 21 September – 6 October 1999 | 16 | 32 → 16 | 16 | ||
| 26 October – 11 November 1999 | 8 | 16 → 8 | none | ||
| 14 and 21 March 2000 | 8 | 8 → 4 | none | ||
| 4 and 18 April 2000 | 4 | 4 → 2 | none | ||
| 2 and 16 May 2000 | 2 | 2 → 1 | none | ||
| Tie no | Home team | Score | Away team | |
|---|---|---|---|---|
| 1 | RNK Split | 3–2 | TŠK Topolovac | |
| 2 | Koprivnica | 3–1 | Valpovka | |
| 3 | Pomorac Kostrena | 1–1 (aet) (3–4 p) | Marsonia | |
| 4 | Čazmatrans | 7–0 | Podravac Virje | |
| 5 | Mosor | 2–0 | Čakovec | |
| 6 | Špansko | 4–1 | Olimpija Osijek | |
| 7 | Duga Resa | 0–1 (aet) | Omladinac Novo Selo Rok | |
| 8 | Zagorec Krapina | 4–1 | Dinara Knin | |
| 9 | Pazinka | 1–2 | Neretva | |
| 10 | Amater Slavonski Brod | 1–4 | Vukovar '91 | |
| 11 | Moslavac Popovača | 2–1 | Dubrava | |
| 12 | BSK Buk | 5–0 | Hajduk Hercegovac | |
| 13 | Mladost 127 | 0–1 | Uljanik Pula | |
| 14 | Pakoštane | 2–4 | Nehaj Senj | |
| 15 | Sloboda Varaždin | 3–0 | PIK Vrbovec | |
| 16 | Ivančica Ivanec | 0–2 | Radnik Velika Gorica |
| Tie no | Home team | Score | Away team | |
|---|---|---|---|---|
| 1 | Bjelovar | 2–1 (aet) | Dubrovnik | |
| 2 | Neretva | 2–1 | Inker Zaprešić | |
| 3 | Moslavac Popovača | 0–8 | Hajduk Split | |
| 4 | Koprivnica | 1–2 (aet) | Varteks | |
| 5 | Uljanik Pula | 0–2 | NK Zagreb | |
| 6 | Čazmatrans | 1–2 | Cibalia | |
| 7 | Vukovar '91 | 0–1 | Slaven Belupo | |
| 8 | Nehaj Senj | 2–2 (aet) (3–2 p) | Zadarkomerc | |
| 9 | Radnik Velika Gorica | 1–2 | Rijeka | |
| 10 | Mosor | 0–0 (aet) (6–5 p) | Segesta | |
| 11 | Sloboda Varaždin | 1–2 | Hrvatski Dragovoljac | |
| 12 | BSK Buk | 0–10 | Croatia Zagreb | |
| 13 | Zagorec Krapina | 3–1 | Belišće | |
| 14 | Špansko | 1–2 | Šibenik | |
| 15 | RNK Split | 0–4 | Marsonia | |
| 16 | Omladinac Novo Selo Rok | 2–3 | Osijek |
| Tie no | Home team | Score | Away team | |
|---|---|---|---|---|
| 1 | Cibalia | 2–1 (aet) | Hrvatski Dragovoljac | |
| 2 | Nehaj Senj | 0–1 (aet) | Rijeka | |
| 3 | Neretva | 0–6 | NK Zagreb | |
| 4 | Hajduk Split | 3–1 | Šibenik | |
| 5 | Bjelovar | 1–3 | Osijek | |
| 6 | Zagorec Krapina | 0–1 | Varteks | |
| 7 | Mosor | 0–2 | Slaven Belupo | |
| 8 | Croatia Zagreb | 4–0 | Marsonia |
|}
Dinamo Zagreb won 6–1 on aggregate.----Hajduk Split won 4–3 on aggregate.
See main article: 2000 Croatian Football Cup final.
Hajduk Split won 2–1 on aggregate.