Born in Foz do Iguaçu, Paraná, Jhonnathan joined Santos' youth setup in March 2018, from Inter de Limeira.

He made his first team debut for Peixe on 3 March 2021, coming on as a second-half substitute for Wagner Leonardo in a 1–1 Campeonato Paulista home draw against Ferroviária.

[5] After failing to appear in any further match for the first team, he was loaned to Série C side Brasil de Pelotas on 20 June 2022.

[7] He scored his first professional goal the following 8 February, netting the winner in a 1–0 Campeonato Potiguar away success over Força e Luz.

[10] On 13 December 2024, Jhonnathan signed a permanent two-year deal with Chape.