| Competition: | Druga HNL |
| Season: | 2006–07 |
| Promoted: | Inter Zaprešić (champions) Zadar (playoff winners) |
| Relegated: | Naftaš HAŠK Koprivnica Bjelovar Čakovec |
| League Topscorer: | Zdravko Popović (30) |
| Matches: | 240 |
| Total Goals: | 747 |
| Prevseason: | 2005–06 |
| Nextseason: | 2007–08 |
The 2006–07 Druga HNL season was the 16th since its establishment. The first placed team were Inter Zaprešić and the last three clubs were relegated to Treća HNL.
| Position | Player | Club | Goals |
|---|---|---|---|
| 1 | Zdravko Popović | Croatia Sesvete | 30 |
| 2 | Bernard Gulić | Inter Zaprešić | 19 |
| 3 | Ivan Lišnić | Belišće / Hrvatski Dragovoljac | 18 |
| 4 | Igor Kolarić | Belišće | 15 |
| 5 | Danko Cerovečki | Moslavina | 13 |
| 6 | Petar Krpan | Inter Zaprešić | 11 |
| 7 |  Glauver Aranha Pinheiro | Imotski | 10 |
| Danijel Zlatar | Hrvatski Dragovoljac | 10 | |
| Ivica Karabogdan | Pomorac | 10 | |
| Goran Burčul | Zadar | 10 | |