The 61-year-old Colombian, who took them to their first ever World Cup quarter-final in Brazil, has cited a difference of opinion with the Costa Rican FA for his reason to leave.
“I realised I would not be able to count on conditions to carry out my work,” he said in a statement on his own personal website.
“So it wasn't possible to reach an agreement to renew my contract."
Pinto, who has managed some 14 different teams including his native Colombia and a previous stint with Costa Rica, took charge of the country for a second time in 2011.
He led them to World Cup qualification for only the fourth time in their history and navigated his side through the supposed ‘group of death’ which contained Italy, England and Uruguay.
Costa Rica then beat Greece 5-3 on penalties after a 1-1 draw in extra time and were beaten by third-placed team Netherlands 4-3 on penalties after a superb effort in the last eight.