The 1999–2000 season of the Swiss Nationalliga contained two divisions, each with twelve clubs.
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 first eight teams of the NLA then competed in the championship group and played a further double round-robin.
They took half of the points (rounded up to complete units) gained in the Qualification as bonus with them.
The teams took half of the points (rounded up to complete units) gained in the qualification as bonus with them.