A Vitória youth graduate, Rafaelson was accused of having an illegal age in April 2015,[2] a claim which was later dismissed by the club.[3] He was promoted to the first team in September, by manager Vagner Mancini.[4]
Rafaelson made his professional debut on 5 September 2015, coming on as a second-half substitute for Robert in a 2–1 home loss against Botafogo for the Série B championship. His first goal came on 31 October, netting the last in a 3–2 home loss against Náutico. He contributed with seven appearances during the campaign, as his side achieved promotion to Série A.
On 30 June 2016, Rafaelson made his top tier debut, replacing Tiago Real in a 3–2 home win against Sport Recife.
On 13 April 2019, Rafaelson moved to Denmark and joined Næstved.[5] Næstved announced on 12 January 2020, that they had sold Rafaelson to Nam Định in the V.League 1.[6] After one season at Nam Định, despite his good form, the club was unable to keep him due to financial difficult, leading him to join V.League 1 fellow SHB Đà Nẵng, where he also stayed for only season.[7]
In September 2021, Rafaelson was transferred to Topenland Bình Định.[8] On 3 September 2022, he scored his first hattrick in V.League 1 in to help his team defeat the league's leading team Hanoi FC 3–0.[9] He later lead his team to the 2022 Vietnamese Cup final, scoring a hattrick in the semi-final game against Đông Á Thanh Hóa.[10] In the 2023 season, Rafaelson became the league top scorer, netting a total of 16 goals and was named in the team of the season.[11]
On 28 August 2023, after his contract with Topenland Bình Định expired, Rafaelson made his return to Nam Định.[12] On 26 May 2024, he scored five goals in a 5–2 victory of Thép Xanh Nam Định FC against Đông Á Thanh Hóa, which tied the record for most goals scored by a single player in a single game in V.League 1 with Hoàng Anh Gia Lai's Nguyễn Đình Việt back in 2007. On 25 June 2023, Rafaelson netted a hattrick in a 5–1 league win against Khánh Hòa, thus securing the first national league title for Nam Định since 1985.[13] He finished the season as the league's top scorer with 31 goals, thus broke the record for most goals scored by a single player in a single V.League 1 season, previously held by Lê Huỳnh Đức (25 goals).[14]