In 2005, he was brought in by Trabzonspor as a replacement for Australian goalkeeper Michael Petkovic. He has previously played in Brazil for Cruzeiro and Botafogo. After four year stint in Turkey with Trabzonspor and Konyaspor, he returned to Botafogo in 2009, where he easily became an important part of the team, saving Botafogo from the relegation in 2009 with great performances. His success did not stop in 2010, when O Glorioso beat Flamengo in the finals of Campeonato Carioca with Jefferson saving a penalty from Adriano. He is considered the best Botafogo's keeper of the last few years. Having been elected on the Team of The Year in the Brazilian National Championship ("Brasileirão"), Jefferson is considered the best keeper in the country and a strong candidate for the Seleção's number 1 spot in 2014.
On July 2011, he was called up to the Brazil national team for the 2011 Copa América. However he did not make any appearance in the competition. On September 14, 2011, he made his first international appearance for Brazil in the first leg of the Superclásico de las Américas matches against Argentina. In the second match of the tournament, he was the first choice once again and made some crucial saves, being regarded as one of the best players, as Brazil beat Argentina for 2-0. On October 7, 2011, he replaced Julio César, injured during the game, against Costa Rica and played for 19' minutes, making this his third appearance for the National Team.