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 2009 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 and runner-up of the National Stage will be promoted to the First Division.
The National Stage started on November 8. This stage had two knockout rounds and four-team group stage. The winner will be promoted to the First Division and the runner-up of the National Stage will be promoted to the Segunda División Peruana.