[2] Filipe Augusto made his professional debut on 29 February 2012, coming on as a substitute for Magno Cruz in a 5–1 home win against Camaçari in the Campeonato Baiano.

On 18 June 2012, Filipe Augusto signed with Primeira Liga side Rio Ave for five years and a €2.2 million fee.

His first match in the UEFA Europa League occurred on 31 July 2014, when he featured 75 minutes in a 1–0 away victory over IFK Göteborg in the third qualifying round.

[5] On 1 September 2014, Filipe Augusto moved to Valencia from Spain in a season-long loan deal, alongside manager Nuno Espírito Santo.

[18] On 23 February 2023, Filipe Augusto returned to Brazil after nearly eleven years, signing for Cuiabá of the Campeonato Brasileiro Série A.