The Apertura tournament was played in a two-round all-play-all system, with the champion being the team with the most points at the end of the two rounds.
The Clausura tournament was played in a single all-play-all system. At the end, the top eight teams qualified to a playoff stage to determine the Clausura champion.
The top eight teams qualified to this stage and were given bonus points based on their final standing in the table. Two groups of four teams were made, with the top two of each group advancing to a playoff stage.
Olimpia wins the Clausura tournament final by aggregate score of 4–1.
National championship game
Since Olimpia won both the Apertura and Clausura tournaments they were declared as the national champions and no playoff game was played.
To determine the second place an extra game between the Apertura runners-up (Sol de America) and the Clausura runners-up (Guarani) was played. Guaraní won the game and were declared runners-up of 2000 (aggregate score of 5–4; first leg 3–1 win by Sol, second leg 4–1 win by Guarani).
Relegation / Promotion
Universal automatically relegated to the second division after finishing last in the average points table based over a three-year period.
Libertad promoted to the first division by winning the second division tournament.