| Season | 1998–99 |
|---|---|
| Champions | SC Freamunde |
| Promoted |
SC Covilhã SC Freamunde Imortal DC |
| Relegated | 12 teams |
|
← 1997–98
|
|
The 1998–99 Segunda Divisão season was the 65th season of the competition and the 49th season of recognised third-tier football in Portugal.
The league was contested by 54 teams in 3 divisions with SC Covilhã, SC Freamunde and Imortal DC winning the respective divisional competitions and gaining promotion to the Liga de Honra. The overall championship was won by SC Freamunde.