The national championship was divided into two tournaments; the Torneo Regional and Torneo Descentralizado. The winners of each tournament faced off in the season final and received the berths for the 1987 Copa Libertadores. The Torneo Regional divided the teams into four groups; Metropolitan, North, Central, and South. Each group had its teams advance to the Liguilla Regional, the Torneo Descentralizado and the División Intermedia. The Liguilla Regional determined the Regional champion. The Descentralizado divided the teams in three groups and the top two in each group advanced to the Descentralizado Liguilla which decided the Descentralizado champion. The División Intermedia was a promotion/relegation tournament between first and second division teams. Teams received two points for a win and one point for a draw. No points were awarded for a loss.
The four group winners and the second placed team in the Metropolitan group qualified directly to the quarter-finals. The remaining qualified teams started in the preliminary round to determine the 3 remaining quarter-finalists. Numbers in parentheses indicate a penalty shootout result. The Regional winner qualified to the 1987 Copa Libertadores and advanced to the Final of the season.