It was founded as a village by the Portuguese in 1658. Despite the date of its foundation, there's a previous record that a famous navigator left Honfleur, Normandy in France by the year of 1503 and arrived at São Francisco do Sul, at the Bay of Babitonga, Jean Binot Paulmier De Gonneville is also recognised by many historians as one of the first, if not the first person to step and discover Sao Francisco's city. It is situated on the northern end of the Island of São Francisco at the entrance to the Babitonga Bay.
São Francisco do Sul is an important part of the Brazilian infrastructure. It provides large bulk shipping facilities and is served by the major container shipping lines connecting with the South American east and west coasts, Africa, Asia, North and Central America, the Caribbean and Europe.
During the past decade, São Francisco do Sul has become a popular tourism destination for South American and international guests. The municipality contains the 6,667 hectares (16,470 acres) Acaraí State Park, created in 2005.