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. The league games started 18 September 1999.[1]
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.[3]
Updated to match(es) played on 2 July 2000. Source: [citation needed] Notes:
^Motagua qualified to the 2001 Copa Interclubes UNCAF as winner of both Apertura and Clausura tournaments. They were also invited to the 2001 CONCACAF Giants Cup as having the best attendances in the 1999–2000 season.
^Olimpia qualified to the 2001 Copa Interclubes UNCAF as best non-champion performance.