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The club was founded on April 12, 1950, by engineers of Estrada de Ferro Araraquara (meaning Araraquara Railroad). Antônio Tavares Pereira Lima was chosen as the club's first president. Initially the club's colors were to be blue and white, like the Rio de Janeiro city team. However, these colors were not very popular, and were changed to carmine and white, like the Juventus ones.

On May 13, 1951, the club played their first match ever. The club beat Mogiana of Campinas 3–1. The club's first goal was scored by Fordinho in that match. On May 20, 1951, the club played their second match, in Taquaritinga city. It was also the club's first defeat. Linense, of Lins, beat Ferroviária 2–1. On June 10, 1951, Ferroviária's stadium, called Estádio Fonte Luminosa, was inaugurated. In the inaugural match, Vasco da Gama, of Rio de Janeiro, beat Ferroviária 5–0. On July 1, 1951, Ferroviária played their first match against a club from the same city. Ferroviária was defeated by Paulista (Araraquara) 4–0.

On April 15, 1956, Ferroviária beat Botafogo of Ribeirão Preto 6–3 in the Campeonato Paulista Second Division final stage (disputed by eight teams playing against each other twice), and won the title and the promotion to the following year's first division. In the last match of the competition, Ferroviária beat Portuguesa Santista 5–4.

In 1983, Ferroviária competed in the Brazilian Série A, finishing in the 12th position. In 1994, the club was the runner-up of the Brazilian Série C, after losing to Novorizontino 1–0 in the first leg, at home, and 5–0 in the second leg, in Novo Horizonte. The club was promoted to the following year's second division.

From 1994 until 1996, the Ferroviária participated in the top division of São Paulo state championship, having Otavio Augusto (Otavio Braga) as their topscore in 1994 with 8 goals and in 1996 with 6 goals.