Colombian Pinto, 61, had coached “Los Ticos” since 2011, leading them to an historic World Cup quarter-final run in Brazil.
Costa Rica lost to the Netherlands on penalties but they were never beaten in open play despite facing three World Cup-winners as well as former European champions Greece.
The tiny Central American nation were written off after being drawn in arguably the tournament`s toughest group, but they shocked both Uruguay and Italy and drew against England.
In the round of 16, they played for an hour with 10 men before beating Greece on penalties, and they held off the Netherlands before being shaded on spot-kicks.
In a coaching career spanning 30 years Pinto has led clubs in Colombia and Peru.
He first coached Costa Rica in 2004-2005, followed by the Colombian national side from 2007-2008. He returned to Costa Rica in 2011.
Pinto said that he had not yet decided on his future plans.