The tournament has 5 stages. The first four stages are played as mini-league round-robin tournaments, except for third stage in region IV, which is played as a knockout stage. The final stage features two knockout rounds and a final four-team group stage to determine the two promoted teams.
The 2003 Peru Cup started with the District Stage (Spanish: Etapa Distrital) on February. The next stage was the Provincial Stage (Spanish: Etapa Provincial) which started, on June. The tournament continued with the Departamental Stage (Spanish: Etapa Departamental) on July. The Regional Staged followed. The National Stage (Spanish: Etapa Nacional) started on November. The winner of the National Stage will be promoted to the First Division.
Departmental Stage
The following list shows the teams that qualified for the Regional Stage.
The National Stage started in November. The winners of the National Stage will be promoted to the 2004 Torneo Descentralizado. On every stage qualification is decided by points, no matter the goal difference. Third match played in neutral ground.