The ANAPROF 1999–2000 season was the twelfth season since its establishment. It began on August 1, 1999, and ended on January 30, 2000. 10 teams competed in the league, 9 of which returned from the previous season and 1 of which was promoted from Primera A.
Tauro were crowned champions after defeating Plaza Amador 2-0 in the Rommel Fernández becoming Tauro's fifth title in its history. After clinching this title Tauro earned the Panama 1 spot in the 2001 season of the Copa Interclubes UNCAF while Plaza Amador earned the Panama 2 spot as the runner-up.
Previous to the start of the season there was a championship that went on from April to July amongst the participating teams to determine who would play in the 2000 season of the Copa Interclubes UNCAF; the 1999–2000 Campeonato Apertura. Panamá Viejo was crowned champion on July 2 after defeating Tauro 2-0.
Source: [citation needed] Legend: Blue = home team win; Yellow = draw; Red = away team win. Notes:
^The eighteenth-round game between Chiriquí-Eurokickers was eliminated due both to its irrelevance in the standings as both teams were already safe from relegation and had no chances of qualifying to the final round, and also to eliminate the expenses of traveling to Chiriquí.[1]
Note: The Semifinal 2 game between Tauro-Árabe Unido was originally played on January 23 at 1:30 PM (UTC-5) but was suspended after the end of the first half of extra time after a group of Árabe Unido's fans invaded the field, Tauro was leading the scoreboard 3-1 at the time. The two periods of extra time were replayed the next day.[2]