| Season: | 1999–2000 |
| Winners: | Dinamo Zagreb 6th Croatian title 10th domestic title |
| League Topscorer: | Tomislav Šokota (21) |
| Matches: | 198 |
| Total Goals: | 534 |
| Average Attendance: | 2,470 |
| Nextseason: | 2000–01 |
The 1999–2000 Croatian First Football League was the ninth season of the Croatian First Football League, the national championship for men's association football teams in Croatia, since its establishment in 1992. The season started on 24 July 1999 and ended on 13 May 2000. Dinamo Zagreb (Croatia Zagreb in fall season) were the defending champions, having won their ninth championship title the previous season, and they defended the title again, after a win against Rijeka on 6 May 2000.
The schedule consisted of three rounds. During the first two rounds, each team played each other once home and away for a total of 22 matches. The pairings of the third round were then set according to the standings after the first two rounds, giving every team a third game against each opponent for a total of 33 games per team.
| Rank | Player | Club | Goals |
|---|---|---|---|
| 1 | Tomo Šokota | Croatia Zagreb | 21 |
| 2 | Ivan Bošnjak | Cibalia Vinkovci | 16 |
| 3 | Boško Balaban | Rijeka | 15 |
| 4 | Josip Šimić | Croatia Zagreb | 14 |
| 5 | Mate Baturina | Hajduk Split | 13 |
| Stanko Bubalo | Osijek | ||
 Marijo Dodik | Slaven Belupo | ||
| 8 | Klaudio Vuković | Šibenik | 12 |
| 9 | Ivan Leko | Hajduk Split | 11 |
| 10 | Vlatko Đolonga | Hrvatski Dragovoljac | 10 |
| Admir Hasančić | Rijeka | ||
 Amarildo Zela | Vukovar '91 |