| Competition: | Regionalliga |
| Season: | 1999–2000 |
| Winners: | VfL Osnabrück (N) 1. FC Union Berlin (NO) 1. FC Saarbrücken (W/SW) SSV Reutlingen (S) |
| Promoted: | 1. FC Saarbrücken SSV Reutlingen VfL Osnabrück LR Ahlen |
| Relegated: | 39 teams |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Regionalliga was the sixth season of the Regionalliga as the third tier of German football. It was also the last season to be competed in four divisions. Teams were not only competing for promotion to the 2. Bundesliga, but also to qualify for the new two-division Regionalliga.
As in the previous seasons there were four divisions: Nord, Nordost, West/Südwest and Süd. Each division comprised 18 teams, with the exception of the West/Südwest division that had 20.
VfL Osnabrück was promoted to 2nd Bundesliga by beating 1. FC Union Berlin in the play-offs.
VfB Lübeck, Eintracht Braunschweig, SV Wilhelmshaven, SV Werder Bremen Amateure and Lüneburger SK qualified for the new two-division Regionalliga.
The remaining teams were relegated to the Oberliga.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Daniel Bärwolf | VfB Lübeck | 25 |
| Marinus Bester | Lüneburger SK | ||
| 3. | Horst Elberfeld | BV Cloppenburg | 25 |
| 4. | Christian Claaßen | VfL Osnabrück | 18 |
| 5. |  Jacek Janiak | VfL Osnabrück | 17 |
| Ioan Perdei | 1. SC Göttingen 05 | ||
| 7. | Markus Erdmann | Arminia Hannover | 16 |
| 4. | Jörg Ahrends | Holstein Kiel | 13 |
| Uwe Harttgen | Werder Bremen (A) | ||
| Joakim N'Tsika-Compaigne | Hamburger SV (A) | ||
| Mark Pomorin | FC St. Pauli (A) | ||
 Stefan Rusnak | BV Cloppenburg | ||
| Dirk Weetendorf | Eintracht Braunschweig | ||
1. FC Union Berlin remains in the Regionalliga, as the club could not secure promotion in the play-off against VfL Osnabrück.
1. FC Union Berlin took part in the play-offs against LR Ahlen and SC Pfullendorf, but could not win promotion.
Dresdner SC, FC Erzgebirge Aue, FC Carl Zeiss Jena, SV Babelsberg 03, FC Sachsen Leipzig and Rot-Weiß Erfurt qualified for the new two-division Regionalliga.
The remaining teams were relegated to the Oberliga.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Hendryk Lau | SV Babelsberg 03 | 16 |
| 2. | Steffen Menze | 1. FC Union Berlin | 14 |
| 3. | Jörg Kirsten | Erzgebirge Aue | 13 |
| 4. |  Harun Isa | Erzgebirge Aue | 12 |
| Sven Kretschmer | Hertha BSC (A) | ||
| Rocco Milde | FSV Zwickau / Dresdner SC | ||
| 4. | Alexander Dürr | VfB Leipzig | 11 |
| Aleksandar Jović | Carl Zeiss Jena | ||
 Adolphus Ofodile | 1. FC Magdeburg | ||
| Kostas Pantios | Tennis Borussia Berlin (A) | ||
 Sergio Sánchez | Dresdner SC |
1. FC Saarbrücken was promoted to the 2nd Bundesliga.
LR Ahlen won promotion to the 2nd Bundesliga by beating 1. FC Union Berlin and SC Pfullendorf in the play-offs.
Teams ranked from 3 to 11 qualified for the new two-division Regionalliga.
The remaining teams were relegated to the Oberliga.
| Player | Club | Goals | |
|---|---|---|---|
| 1. | Marius Ebbers | SG Wattenscheid 09 | 23 |
| 2. |  Daniel Teixeira | KFC Uerdingen | 22 |
| 3. | Mario Krohm | LR Ahlen | 21 |
| 4. | Sambo Choji | 1. FC Saarbrücken | 20 |
| 5. | Amaechi Ottiji | FC Gütersloh / Sportfreunde Siegen | 19 |
| 6. |  Ersin Demir | Bayer Leverkusen (A) | 18 |
| 7. | Marek Czakon | SV Elversberg | 17 |
| 8. | Sascha Wolf | Rot-Weiß Essen | 16 |
| 9. | Tobias Weis | 1. FC Kaiserslautern (A) | 14 |
| 10. | Jan Majewski | VfL Bochum (A) | 13 |
| Ganiyu Shittu | Fortuna Düsseldorf | ||
 Raffael Tonello | Sportfreunde Siegen |
SSV Reutlingen 05 was promoted to the 2. Bundesliga. SC Pfullendorf took part in the play-offs against 1. FC Union Berlin and LR Ahlen, but could not win promotion.
Teams ranked 3 to 13 qualified for the new two-division Regionalliga.
Teams ranked below 13 were relegated to the Oberliga.
FC Augsburg and Karlsruher SC Amateure were forcibly relegated.
| Player | Club | Goals | |
|---|---|---|---|
| 1. |  Olivier Djappa | SSV Reutlingen | 36 |
| 2. | Neno Rogošić | VfR Aalen | 18 |
| 3. | Marko Barlecaj | SC Pfullendorf | 17 |
| Ivica Magdić | SC Pfullendorf | ||
| 5. | Zdenko Juric | VfR Mannheim | 16 |
| Sascha Maier | Wacker Burghausen | ||
| 7. | Ralf Becker | SSV Reutlingen | 15 |
| 8. | Patrick Würll | Bayern Munich (A) | 14 |
| 9. | Markus Lützler | Wacker Burghausen | 13 |
| Andreas Rüppel | FSV Frankfurt | ||
| Antonio Di Salvo | Bayern Munich (A) |
The champions of the Regionalliga Nord (VfL Osnabrück) and Regionalliga Nordost (1. FC Union Berlin) faced each other in a two-legged playoff. Osnabrück, as winners, were promoted to the 2. Bundesliga, while Union were given another chance at promotion in round 2.[1]
1. FC Union Berlin faced the runners up of the Regionalliga West/Südwest (LR Ahlen) and Regionalliga Süd (SC Pfullendorf) in a round-robin tournament. Ahlen won this mini-league, and took the final promotion place.[2]
Kickers Emden, champions of the Oberliga Niedersachsen/Bremen, beat TuS Felde, Oberliga Schleswig-Holstein champions in a playoff to face Lüneburger SK, who had finished 6th in the Regionalliga Nord. Lüneburg won 3–1 on aggregate to stay in the Regionalliga.
FC Schönberg 95, champions of the NOFV-Oberliga Nord, beat FSV Hoyerswerda, NOFV-Oberliga Süd champions in a playoff to face Rot-Weiß Erfurt, who had finished 7th in the Regionalliga Nordost. Erfurt won 4–2 on aggregate to stay in the Regionalliga.
SV Elversberg, who had finished twelfth in the Regionalliga West/Südwest, entered a mini-league with VfB Hüls (Oberliga Westfalen champions), Wuppertaler SV (Oberliga Nordrhein champions) and Borussia Neunkirchen (Oberliga Südwest champions) for a place in the Regionalliga. Elversberg won the league with a 100% record.
No team from the Oberliga Hessen entered qualification, so the champions of the Oberliga Baden-Württemberg (SV Sandhausen) and Bayernliga (Jahn Regensburg) played off in the first round. Regensburg won 5–6 on aggregate, and went on to play FSV Frankfurt, winning 6–3 on aggregate to earn promotion to the Regionalliga Süd.