Born in Dourados, Mato Grosso do Sul, João Paulo joined Santos' youth setup in late 2011, after representing São Carlos, Itaporã (where he was a part of the first team squad at the age of just 16),[2] Grêmio (where he spent just four months in a trial period)[3] and Sete de Setembro.

In March 2015, after Vanderlei's injury, João Paulo was inscribed in the year's Campeonato Paulista as a third-choice behind Vladimir and Gabriel Gasparotto.

[6] João Paulo made his unofficial first team debut on 8 October 2016, playing the last 20 minutes and saving a penalty in a 1–1 friendly draw against Benfica.

[7] On 16 July of the following year, after both Vanderlei and Vladimir were injured, he made his professional – and Série A – debut by starting in a 0–0 away draw against Vasco da Gama.

[9] He started to appear more regularly during the 2020 season, as Vanderlei left, Vladimir was injured and Everson took a legal action against the club,[10] and renewed his contract until 2025 on 8 September 2020.