Starting from 1842, small villages were established in the area of the Tietê River. In 1848 Manoel dos Santos Simões and his two sons, Manuel Leonel dos Santos and João Leonel dos Santos, established a farm in the parish of Botucatu. They named the farm "Pederneiras" after the large amount of flint stone in the area. In 1865, the settlement became part of the municipality of Lençóis Paulista. Four years later it became a parish with the name "São Sebastião de Alegria". Coffee plantations led to growth of the settlement, and in 1891 it became a separate municipality. In 1895, the town's name was changed back into "Pederneiras".