The 1998–99 Nemzeti Bajnokság II is Hungary's second-level football competition.
The championship was won by Lombard FC Tatabánya and they were also promoted to the 1999–2000 Nemzeti Bajnokság I along with Nagykanizsa and Szeged LC.
Four teams including Salgótarjáni BTC, Tiszavasvári, Soroksár and Soproni FAC were relegated to the 1999–2000 Nemzeti Bajnokság III.
Three teams were relegated to Nemzeti Bajnokság III : Csepel, Dorog and Paks.
The winners and runners-up of the two 1997–98 Nemzeti Bajnokság III series were promoted to NB III: Demecser, Soroksár, Komárom and Tatabánya.