The 1998–99 Regionalliga was the fifth season played in the Regionalliga as the third tier of German football.
As in the previous season, the competition was organized in four divisions: Nord, Nordost, West/Südwest and Süd. Each division had 18 teams with the exception of the West/Südwest division with only 17.
Nord
VfL Osnabrück remained in the Regionalliga, because they lost in the play-offs against Chemnitzer FC. As the loser of the North-Northeast play-offs, Osnabrück competed in another play-off against Eintracht Trier and Kickers Offenbach, but could not qualify for promotion to the 2. Bundesliga.
A preliminary decider was contested between the champions of the North and North-East regions. Chemnitzer FC won on aggregate and so were promoted to the 2. Bundesliga.[1]
The loser of the above tie faced the second placed teams from the South and West/South-West regions for a final promotion place. Kickers Offenbach earned promotion to the 2. Bundesliga.[2]