Pinto managed several teams in Colombia, including Santa Fe and Union Magdalena on two occasions, before joining Club Alianza Lima in 1997. The team was able to win the 1997 Torneo Descentralizado, after an 18-year drought. Afterwards, he left the club and returned to Colombia. After an unsuccessful attempt at coaching Costa Rica in 2004–2005, Pinto returned to Colombia to coach a recently promoted team Corporación Nuevo Cúcuta Deportivo which he led to win their first Colombian National Championship in their history. He was later named as the new coach of the Colombia national football team. His job was highly criticized by the general public after very bad showings against Uruguay and Chile in 2010 World Cup Qualifying matches as well as in the 2007 Copa América. Jorge Luis Pinto took Colombia to one of the best starts in FIFA World Cup Qualifying in Colombian football history, obtaining 10 points out of a possible 16. However, due to several lackluster performances later on, Colombia ended in 7th place and failed to qualify for the 2010 FIFA World Cup. In 2011, he became manager of Costa Rica again, and on 10 September2013 qualified for the 2014 FIFA World Cup in Brazil. Costa Rica ended in second place in 2014 World Cup qualification. He was voted as CONCACAF's best coach of 2014 after the World Cup, beating United States head coach Jürgen Klinsmann. In the 2014 FIFA World Cup, Pinto secured a 3–1 victory for Costa Rica over Uruguay and another 1–0 victory over Italy. After a 0–0 draw against England, Costa Rica finished first in what many called the "Group of Death", the second time Costa Rica made it to the World Cup Round of 16. On 29 June 2014, Costa Rica defeated Greece on penalties and went through to the quarter finals of the 2014 World Cup. His team eventually lost on penalties to the Netherlands after a goalless draw. In December 2014, he became manager of the Honduras. Pinto took his team into the two leg intercontinental playoff against Australia for a place at the 2018 FIFA World Cup in Russia. However, Honduras lost to Australia 3–1 on aggregate over the two legs and Pinto later stepped down as Honduras coach. In July 2018 he was on a 4-man shortlist for the vacant Egyptian national team manager job.
