The 1998–99 Segunda Divisão season was the 65th season of the competition and the 49th season of recognised third-tier football in Portugal.
[1] 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.
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