2006–07 Croatian Second Football League
| Season | 2006–07 | 
|---|---|
| Promoted | 
Inter Zaprešić (champions) Zadar (playoff winners)  | 
| Relegated | 
Naftaš HAŠK Koprivnica Bjelovar Čakovec  | 
| Matches played | 240 | 
| 
 ← 2005–06  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.
Teams competing in 2006-07
- Belišće
 - Bjelovar
 - Croatia Sesvete
 - Čakovec
 - Hrvatski Dragovoljac
 - Imotski
 - Inter Zaprešić
 - Koprivnica
 - Marsonia
 - Moslavina
 - Mosor
 - Naftaš HAŠK
 - Pomorac
 - Solin
 - Vukovar '91
 - Zadar
 
League table
| Pos | 
Team | 
Pld | 
W | 
D | 
L | 
GF | 
GA | 
GD | 
Pts | Qualification or relegation | 
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Inter Zaprešić (C) (P) | 30 | 21 | 5 | 4 | 60 | 28 | +32 | 68 | Promotion to 2007–08 Prva HNL | 
| 2 | Zadar (O) (P) | 30 | 20 | 5 | 5 | 55 | 25 | +30 | 65 | Relegation play-off | 
| 3 | Croatia Sesvete | 30 | 18 | 5 | 7 | 67 | 38 | +29 | 59 | |
| 4 | Hrvatski Dragovoljac | 30 | 18 | 4 | 8 | 60 | 25 | +35 | 58 | |
| 5 | Solin | 30 | 16 | 5 | 9 | 58 | 33 | +25 | 53 | |
| 6 | Imotski | 30 | 12 | 8 | 10 | 41 | 44 | −3 | 44 | |
| 7 | Belišće | 30 | 11 | 9 | 10 | 46 | 40 | +6 | 42 | |
| 8 | Pomorac | 30 | 11 | 9 | 10 | 53 | 51 | +2 | 42 | |
| 9 | Vukovar '91 | 30 | 9 | 8 | 13 | 40 | 42 | −2 | 35 | |
| 10 | Naftaš HAŠK (R) | 30 | 8 | 11 | 11 | 44 | 49 | −5 | 351 | |
| 11 | Mosor | 30 | 9 | 8 | 13 | 37 | 46 | −9 | 35 | |
| 12 | Marsonia | 30 | 9 | 7 | 14 | 38 | 50 | −12 | 34 | |
| 13 | Moslavina | 30 | 9 | 6 | 15 | 44 | 57 | −13 | 33 | Relegation to Treća HNL | 
| 14 | Koprivnica (R) | 30 | 7 | 8 | 15 | 42 | 66 | −24 | 29 | |
| 15 | Bjelovar (R) | 30 | 4 | 6 | 20 | 25 | 66 | −41 | 18 | |
| 16 | Čakovec (R) | 30 | 4 | 4 | 22 | 37 | 87 | −50 | 16 | 
Updated to games played on 20 May 2007.
Source: rsssf.com
Rules for classification:
1) points; 2) goal difference; 3) number of goals scored
1Naftaš HAŠK were refused a 2nd level license for 2007–08 season, due to this, Moslavina remained at 2nd level.
(C) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round. 
Only applicable when the season is not finished: 
(Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.
Promotions and relegations in 2006
- Promoted to Prva HNL: NK Šibenik
 - Relegated from Prva HNL: NK Inter Zaprešić
 - Promoted from the Treća HNL: NK Moslavina
 
Top scorers
| Position | Player | Club | Goals | 
|---|---|---|---|
| 1 |   | 
Croatia Sesvete | 30 | 
| 2 |   | 
Inter Zaprešić | 19 | 
| 3 |   | 
Belišće / Hrvatski Dragovoljac | 18 | 
| 4 |   | 
Belišće | 15 | 
| 5 |   | 
Moslavina | 13 | 
| 6 |   | 
Inter Zaprešić | 11 | 
| 7 |   | 
Imotski | 10 | 
|   | 
Hrvatski Dragovoljac | 10 | |
|   | 
Pomorac | 10 | |
|   | 
Zadar | 10 | |