The tournament has five 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 (Spanish: Etapa Distrital) on February. The next stage was the Provincial Stage (Spanish: Etapa Provincial) which started, on June. The tournament continued with the Departmental 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.
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.
The second leg was abandoned after 81 minutes because of a brawl started by Bolognesi players. The F.P.F. (Peruvian Football Federation) declared the match ended by 3-1; and as it should have been a penalty shootout, I.M.I. was declared shootout winner by 2-0, and hence 1998 champions.