The club was founded on February 4, 1984 and was called Futebol Clube Esperança (FC Esperança). In 1996, the club changed its name to Sanjoanense after Saint John, the patron saint of Porto Novo.
The team is the only one of the four teams in the division that never won any title since the breakup of the island division in 1997. Recently the club cannot afford to compete in the island league due to the financial reasons in the early 2010s.
Together with Santo André, the club withdrew and is absent from the 2015/16 season.