The 1999–2000 Honduran Liga Nacional was the 35th season in the Honduran top division, the tournament was divided into two halves (Apertura and Clausura) and it determined the 35th and 36th national champions in the league's history.
[1] The Apertura was the opening half of 1999–2000 season in the Honduran Liga Nacional.
The Clausura tournament of the 1999–2000 season in the Liga Nacional de Fútbol de Honduras started on 11 March 2000 at San Pedro Sula with a scoreless match between C.D.
Note: Motagua (3rd) had the right to play the second leg at home after finishing above Marathón (5th) in the regular season; Marathón however claimed they had to close the series at home after they defeated Platense in the Hexagonal who finished 2nd; eventually Motagua granted home-field advantage in the second leg at San Pedro Sula.
Relegation was determined by the aggregate table of both Apertura and Clausura tournaments.