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.
Source: [citation needed] Legend: Blue = home team win; Yellow = draw; Red = away team win.
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.
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.