Born in Praia Grande, São Paulo, Wagner joined Santos' youth setup in 2009 at the age of nine.

[1] In February 2019, after appearing in the year's Copa São Paulo de Futebol Júnior, he was promoted to the first team by manager Jorge Sampaoli.

[2] Wagner made his first team debut on 7 March 2019, coming on as a second-half substitute for fellow youth graduate Gustavo Henrique in a 4–0 home routing of América-RN, for the year's Copa do Brasil.

[4] Wagner made his Copa Libertadores debut on 20 October 2020, replacing Felipe Jonatan in a 2–1 home win against Defensa y Justicia.

[7] He became a regular starter for the side, and scored his first goal on 26 April in a 2–2 Campeonato Pernambucano home draw against Afogados.