| Competition: | Regionalliga |
| Season: | 1998–99 |
| League Topscorer: | Daniel Bärwolf, Daniel Thioune (26 goals) |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
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.
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.
Kickers Emden, VfL Hasetal Herzlake and Sportfreunde Ricklingen were relegated to the Oberliga.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Daniel Bärwolf | VfB Lübeck | 26 |
| 2. | Daniel Thioune | VfL Osnabrück | 26 |
| 3. | Marinus Bester | Lüneburger SK | 17 |
| 4. | Christian Claaßen | VfL Osnabrück | 16 |
| Carsten Minich | Eintracht Nordhorn | ||
| 4. |  Garip Capin | TuS Celle | 15 |
| Markus Erdmann | Arminia Hannover | ||
| 6. |  Collins Etebu | VfB Oldenburg | 14 |
| Dennis van Dijk | Werder Bremen (A) | ||
| 10. | Hakan Cengiz | Kickers Emden | 12 |
| Mike Göbel | Holstein Kiel | ||
| Geert Goolkate | Eintracht Nordhorn | ||
| Klaus Osterkamp | BV Cloppenburg |
Chemnitzer FC won promotion to the 2. Bundesliga by defeating VfL Osnabrück in the play-offs, Spandauer SV and SD Croatia Berlin are relegated to the Oberliga. Eisenhüttenstädter FC Stahl remains in the league due to the forcible relegation of Spandauer SV.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Rainer Wiedemann | FSV Lok Altmark Stendal | 19 |
| 2. | Veselin Popović | FSV Zwickau | 16 |
| 3. | Steffen Menze | 1. FC Union Berlin | 14 |
| 4. |  Almir Filipović | FC Sachsen Leipzig | 13 |
| 5. | Marco Dittgen | VfB Leipzig | 12 |
| Nico Patschinski | Dynamo Dresden | ||
| 7. | Heiko Brestrich | FC Berlin | 11 |
| Hendryk Lau | SV Babelsberg 03 | ||
| Rocco Milde | FSV Zwickau | ||
| Arnd Spranger | VFC Plauen | ||
| Mirko Ullmann | Chemnitzer FC |
Alemannia Aachen was promoted to the 2. Bundesliga while Eintracht Trier took part in the play-offs against VfL Osnabrück and Kickers Offenbach, but was not promoted. FSV Salmrohr, SpVgg Erkenschwick and FC Remscheid were relegated to the Oberliga while Wuppertaler SV and FC 08 Homburg were forcibly relegated.
| Player | Club | Goals | ||
|---|---|---|---|---|
| 1. | Daniel Graf | 1. FC Kaiserslautern (A) | 19 | |
| 2. | Vlado Papić | Eintracht Trier | 17 | |
| Christian Timm | Borussia Dortmund (A) | |||
| 4. | Zorislav Jonjić | Sportfreunde Siegen | 16 | |
| Gerrit Meinke | Wuppertaler SV | |||
| 6. | Ersin Demir | Bayer Leverkusen (A) | 15 | |
| 7. | Holger Karp | LR Ahlen | 14 | |
| 8. | Carsten Gockel | Preußen Münster | 13 | |
| Frank Wagner | FSV Salmrohr | |||
| 10. |  Antonio Di Salvo | SC Paderborn 07 | 12 |
SV Waldhof Mannheim was promoted to the 2. Bundesliga while Kickers Offenbach took part in the play-offs against VfL Osnabrück and Eintracht Trier and was promoted to the 2. Bundesliga. SC Weismain and SC Neukirchen 1899 were relegated to the Oberliga.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Marijo Marić | SSV Reutlingen | 23 |
| 2. | Oliver Roth | Kickers Offenbach | 16 |
| Thorsten Seufert | 1. FC Schweinfurt 05 | ||
| 4. | Marco Fladung | Borussia Fulda | 13 |
| Fred Klaus | SC Weismain | ||
| Heiko Liebers | SC Neukirchen | ||
| 7. | Marko Barlecaj | 1860 Munich (A) / SC Pfullendorf | 12 |
| Jörg Kirsten | SV Waldhof Mannheim | ||
| Sascha Maier | VfR Mannheim | ||
| Andreas Rüppel | FSV Frankfurt | ||
| Richard Walz | SV Wehen |
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]