Júnior Dutra made his senior debut on 30 May 2008, coming on as a second-half substitute in a 0–0 Campeonato Paulista Série A2 away draw against Oeste; it was also the tournament's final.[2] His professional debut occurred on 8 August, starting in a 3–2 home win against Ceará for the Série B championship.[3]
Júnior Dutra contributed with seven appearances, as his side achieved promotion to Série A after finishing second. He scored his first professional goal on 1 February 2009, netting the first in a 2–0 away win against São Paulo.[4]
Júnior Dutra made his top flight debut on 4 June 2009, starting in a 3–3 home draw against former side Santos. He scored his first goal in the category on 19 August, netting the first in a 2–1 success at Botafogo.[5]
After scoring two goals in 24 league matches, Júnior Dutra moved abroad and joined J1 League side Kyoto Sanga FC, for a fee of R$8 million.[6] An undisputed starter, he suffered relegation with the club during his first season.
In 2012 Júnior Dutra signed for Kashima Antlers, again being an ever-present figure and scoring a career-best eight goals during the campaign, also being crowned champions of the year's J.League Cup. On 10 January 2013 he moved to Europe, after agreeing to an 18-month contract with Lokeren in the Belgian Pro League.[7]
In February 2015 Júnior Dutra switched teams and countries again, after signing for Qatar Stars League side Al-Arabi.[8] On 28 February he scored a hat-trick in a 4–4 away draw against Al Kharaitiyat, and roughly a month later he scored the league's fastest goal by netting in the tenth second in a 1–3 loss at Lekhwiya.[9]
In March 2016 Júnior Dutra rescinded with Al-Arabi, after having unpaid wages.[1] He subsequently represented Vasco da Gama and Avaí back in his homeland.