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 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.