| Season: | 1999–2000 |
| Competition: | Nationalliga A |
| Winners: | St. Gallen 2nd title |
| Relegated: | Delémont |
| League Topscorer: | Charles Amoah (25 goals) |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 season of the Swiss Nationalliga contained two divisions, each with twelve clubs. The top tier was called Nationalliga A (NLA) (French: Ligue Nationale A, Italian: Lega Nazionale A) and the second tier was named Nationalliga B (NLB).
The season was divided into two phases. The first of which was the qualification phase, and within the divisions the teams played a double round-robin, one at home and the other away. The divisions were then split. The first eight teams of the NLA then competed in the championship group and played a further double round-robin. The teams in ninth to twelfth position competed with the top four teams of the NLB in a promotion/relegation group to decide which four teams would play top tier next season. The other eight teams of the second tier competed in a play-out against relegation to the 1. Liga and the last two teams were to be relegated.
At the end of the season FC St. Gallen won the championship.
The first eight teams of the qualification then competed in the Championship Round. They took half of the points (rounded up to complete units) gained in the Qualification as bonus with them.
The teams in the ninth to twelfth positions in Nationalliga A competed with the top four teams of Nationalliga B in a Nationalliga A/B promotion/relegation round.
The last eight teams of the qualification phase competed in the relegation group against relegation to the 1. Liga. The teams took half of the points (rounded up to complete units) gained in the qualification as bonus with them.