The Clausura tournament was played from February to June 2003. C.D. Marathón took revenge a year and a half later and defeated C.D. Motagua in the finals to claim its 4th league title.
Relegation was determined by the aggregated table of both Apertura and Clausura tournaments. On 10 May 2003, C.D. Victoria were relegated to Liga de Ascenso, however they bought Honduras Salzburg's franchise and stayed in first division.
During the Apertura tournament, C.D. Marathón hosted Real C.D. España on week 9, the match was played on 28 September and ended with a 0–2 away win to Real España. During halftime, Real España delayed more than 15 minutes and returned late to play the second half. Marathón alleged and the Board of Discipline annulled the game. A rematch was played on 13 October ending in a 0–0 draw. Such decision affected the final standings which resulted in Marathón owning the third place and sent Real España to fourth.[2]