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| Player | Team | Goals |
|---|---|---|
| A. Volkov | Maardu | 34 |
| A. Jakovenko | Legion | 32 |
| J. Zahharov | Johvi Phoenix | 19 |
| H. Lehtmaa | Paide II | 19 |
| A. Anepaio | JK Tabasalu | 16 |
| R. Mihhalevski | Tartu Kalev | 15 |
| D. Drabinko | Maardu | 13 |
| G. Tsvibelberg | Johvi Phoenix | 13 |
| N. Baljabkin | Narva U21 | 13 |
| Manucho | Maardu | 13 |
| A. Jegorov | Narva U21 | 12 |
| B. Stoyanov | Johvi Phoenix | 12 |
| E. Utgof | Maardu | 12 |
| G. Kruusla | Tartu Kalev | 12 |
| D. Ruus | Legion | 10 |
| M. Minajev | Johvi Phoenix | 10 |
| P. Bahval | Narva U21 | 10 |
| R. Juhanson | Tartu Kalev | 10 |
| A. Taar | Maardu | 9 |
| M. Opp | Kuressaare II | 9 |
| V. Kudriashov | Narva U21 | 9 |
| A. Gusarov | Nõmme United II | 9 |
| P. Corr | Paide II | 9 |
| R. Samulin | Tartu Kalev | 9 |
| K. Pormeister | JK Tabasalu | 8 |
| A. Badamosi | Paide II | 8 |
| S. Reinkort | Paide II | 8 |
| A. Besigirskis | Narva U21 | 8 |
| K. Tomingas | Nõmme United II | 8 |
| R. Leppik | Nõmme United II | 8 |