Born in Campinas, São Paulo state, he started his career in 1967, playing for Ponte Preta, but the best moment in his career was playing for São Paulo, where he won the 1975 Campeonato Paulista, and played 262 matches, having scored six goals. He has also played for Santos, where he won the 1978 Campeonato Paulista, and Juventus.
In July 2009, Nelsinho returned to Japan to manage Kashiwa Reysol. Despite being unable to stave off relegation to J. League Division 2 at the end of the year, the club relented and allowed him to remain in charge. In 2011, Reysol under him won their first ever J. League Division 1 title, making history by becoming the first team to win the championship following promotion. In the same year, Nelsinho Baptista received the J. League Manager of the Year at the J. League awards in Yokohama.