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 1998 Peru Cup started with the District Stage (Template:Lang-es) on February. The next stage was the Provincial Stage (Template:Lang-es) which started, on June. The tournament continued with the Departmental Stage (Template:Lang-es) on July. The Regional Staged followed. The National Stage (Template:Lang-es) started on November. The winner and runner-up 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.
Note: Originally Señor de Puelles (8 pts) won the group. But after a complaint by Hidro, this team received 3 pts from its match against Señor de Puelles, hence obtaining first place.
Region VI
Region VI includes qualified teams from Apurímac, Ayacucho and Huancavelica region.