Zé Rafael began his professional career in Brazil with Coritiba in 2012. In 2014, he was loaned out to Portuguese club Paços de Ferreira, where he played for one season. He then returned to Coritiba and played there until 2016.
In 2016, Zé Rafael transferred to Palmeiras. He has played for the club since then and has been a key player in their success. He has won two Campeonato Brasileiro Série A titles (2016, 2018) and one Campeonato Paulista (2020) with Palmeiras.
Zé Rafael has also represented the Brazil national team at various age levels. He made his debut for the senior team in 2019. He has been included in Brazil's squad for the 2022 World Cup.