| Competition: | Druga HNL |
| Season: | 1999–2000 |
| Winners: | Marsonia |
| Promoted: | Marsonia Čakovec |
| Relegated: | Čazmatrans RNK Split Zagorec Krapina Otok Mladost 127 |
| League Topscorer: | Miroslav Vukić (26) |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Druga HNL was the ninth season of Druga HNL, the second level league in Croatian football.
The format of the league was unchanged from the 1998–99 season. A total of 17 clubs competed in Druga HNL this season, in a double round-robin format (following relegation from 1998–99 Prva HNL, Mladost 127 was supposed to compete in Druga HNL, but the club folded due to financial difficulties and Druga HNL was reduced to 17 teams before the season started).
| Club | City / Town | Stadium | Capacity | 1998–99 result | |
|---|---|---|---|---|---|
| Belišće | Belišće | Gradski stadion Belišće | 4,000 | ||
| Bjelovar | Bjelovar | Gradski stadion Bjelovar | 4,000 | ||
| Čakovec | Čakovec | Stadion SRC Mladost | 8,000 | ||
| Čazmatrans | Čazma | Gradski stadion Čazma | 1,500 | ||
| Croatia Sesvete | Sesvete | Stadion ŠRC Sesvete | 3,500 | ||
| Jadran Poreč | Poreč | Stadion Veli Jože | 2,000 | ||
| Marsonia | Slavonski Brod | Gradski stadion uz Savu | 10,000 | ||
| Mosor | Žrnovnica | Igralište Pricviće | 3,000 | ||
| Orijent | Rijeka | Stadion SC Krimeja | 4,000 | ||
| Otok | Otok | Stadion Otok | 500 | ||
| Pomorac | Kostrena | Stadion Žuknica | 3,500 | ||
| Segesta | Sisak | Gradski stadion Sisak | 8,000 | ||
| Solin | Solin | Stadion pokraj Jadra | 4,000 | ||
| RNK Split | Split | Stadion Park mladeži | 8,000 | ||
| PIK Vrbovec | Vrbovec | Gradski stadion kraj Sajmišta | 3,000 | ||
| Zadarkomerc | Zadar | Stadion Stanovi | 5,860 | ||
| Zagorec Krapina | Krapina | Stadion SRC Podgora | 3,000 |