In the 2004 season of the Esiliiga, the second-tier league of the Estonian football league system, the Tammeka team finished in top position. Tammeka, Tervis and Dünamo won promotion to the Meistriliiga and no team was relegated to the II Liiga.
JK Dünamo Tallinn beat FC Lootus Alutaguse 5–2 on aggregate. Dünamo promoted to Meistriliiga, Lootus relegated to Esiliiga.
Tallinna Jalgpalliklubi beat FC Puuma Tallinn 4–1 on aggregate. TJK stayed in Esiliiga, Puuma in Second Division.
| Pos | Name | Team | Goals | |
|---|---|---|---|---|
| 1 | Oliver Konsa | JK Tammeka Tartu | 25 | |
| 2 | Mihhail Ištšuk | JK Tervis Pärnu | 18 | |
| 3 | Konstantin Butajev | JK Dünamo Tallinn | 17 | |
| 4 | Aleksei Titov | F.C.A. Estel Tallinn | 14 | |
| 5 | Martti Pukk | FC Kuressaare | 13 |