Born in Ponta Grossa, Paraná, Zé Rafael joined Coritiba's youth setup in 2009, aged 16,[1] as an attacking midfielder.

He made his first team debut on 29 April 2012, coming on as a half-time substitute for Rafael Silva in a 3–1 Campeonato Paranaense away win against Roma.

Zé Rafael was definitely promoted to the first team ahead of the 2013 season,[1] and made his Série A debut on 11 August of that year by replacing Lincoln in a 1–0 loss at Vasco da Gama.

[4] Zé Rafael was an undisputed starter during the second division, scoring four goals in 32 appearances as his side finished sixth, three points away from another promotion; highlights included a brace in a 2–1 away win against Vila Nova.

[11] After the arrival of new signing Aníbal Moreno and the proeminence of Richard Ríos, Zé Rafael played most of the 2024 Campeonato Paulista as a left midfielder.