Ponte Preta was founded on August 11, 1900 by Colégio Culto à Ciência students Miguel do Carmo (nicknamed "Migué"), Luiz Garibaldi Burghi, (nicknamed "Gigette") and Antonio de Oliveira (nicknamed "Tonico Campeão"), nearby a black painted wood railroad bridge, so the name Ponte Preta (which means "black bridge", in English). Ponte Preta's first president was Pedro Vieira da Silva.

Ponte Preta is recognized, by FIFA, as one of the first teams in the Americaa to accept black players, since its foundation in 1900. It is also the first countryside team to play a national competition, in 1970.

Pelé's last match in Brazil was against Ponte Preta. On September 2, 1974, at Vila Belmiro stadium, Santos defeated Ponte Preta 2-0.

Ponte Preta lost the Campeonato Paulista final to Corinthians in 1977 in a controversial game that ended in a 2-1 final score. Rui Rey, an important piece of the Ponte Preta team, was shown a red card early in the game for no apparent reason. Ponte Preta were considered the favorites for the championship that year.

The club finished in the third position in the 2011 Série B, and gained promotion to the 2012 Série A