This is a list of Croatian football transfers for the 2008–09 winter transfer window. Only moves featuring at least one Prva HNL club are listed. The winter transfer window officially opened on 1 January 2009, although transfers may have taken place prior to that date. The window closed at midnight on 31 January 2009.
| Date | Name | Moving from | Moving to | Fee | Source |
|---|---|---|---|---|---|
| 08 Dec 2008 | €400,000 | Sportnet.hr | |||
| 12 Dec 2008 | €250,000 | Sportnet.hr | |||
| 12 Dec 2008 | €300,000 | Sportnet.hr | |||
| 15 Dec 2008 |  | €2,200,000 | Sportnet.hr | ||
| 18 Dec 2008 |  | Free transfer | |||
| 18 Dec 2008 |  | €1,500,000 | Sportnet.hr | ||
| 18 Dec 2008 | €450,000 | Sportnet.hr | |||
| 23 Dec 2008 | €800,000 | Sportnet.hr | |||
| 23 Dec 2008 | Undisclosed | Sportnet.hr | |||
| 08 Jan 2009 | €400,000 | Sportnet.hr | |||
| 12 Jan 2009 | Free transfer | Sportnet.hr | |||
| 13 Jan 2009 | Free transfer | Nogometni magazin | |||
| 15 Jan 2009 | Free transfer | Sportnet.hr | |||
| 16 Jan 2009 | €300,000 | Sportnet.hr | |||
| 27 Jan 2009 | Loan | Sportnet.hr | |||
| 29 Jan 2009 | €500,000 | Sportnet.hr | |||
| 30 Jan 2009 | Free transfer | Sportnet.hr | |||
| 03 Feb 2009 | Loan | ||||