Born in Sorocaba, Rafael joined Santos youth system in 2003. In 2010, he was promoted to the first team, but broke his right leg in a split with the centre backDomingos and sidelined for four months. Rafael played in the second half of the match between Santos and the New York Red Bulls in the United States. It was won by Red Bull by 3–1 but Rafael did not concede a goal, the three goals from New York were scored in the first half, when the goalkeeper was Fábio Costa. His debut in the first team for Santos in an official game took place on 2 June 2010, the match between Santos and Cruzeiro in Mineirão, where the score was 0–0. He took the place of Felipe, who had played all previous 37 matches that season. On 20 August2012, Rafael Cabral's right eye started bleeding when he collided with Juan Manuel Martínez in a 2012 Campeonato Brasileiro Série A fixture between Santos and Corinthians. He then recovered and was able to continue the game. Santos won the game 3–2.
On 28 June 2013, Rafael was sold from Santos to Italian side Napoli. The Azzurri paid €5 million for the Brazilian goalkeeper. Rafael made his UEFA Champions League debut against Arsenal in a group stage match in Naples. Napoli won the match 2–0 and Rafael was able to keep a clean sheet against the English side. Nevertheless, Napoli was unable to advance out of the group stages. He was manager Rafael Benítez's first-choice goalkeeper for the 2014–15 season following the departure of the loaned-in Pepe Reina. On 22 December, in the 2014 Supercoppa Italiana in Doha, he gave Napoli victory over Juventus by saving from Simone Padoin in sudden death at the end of a penalty shootout.
On 22 July 2018, Rafael Cabral signed with Sampdoria on a free transfer. On 5 August 2019, U.C. Sampdoria announced that Rafael Cabral’s contract with the club had been terminated by mutual agreement.
Reading
On 6 August 2019, Reading announced the signing of Rafael on a three-year contract. Rafael made his debut against Wycombe Wanderers in the Carabao Cup and saved two penalties in the penalty shootout win. Rafael made his Sky Bet Championship debut against Cardiff City and gained his first clean sheet for the club in a 3–0 victory. He then went on to claim the No. 1 spot, beating out Everton loanee João Virginia and Sam Walker. Rafael’s heroics during consecutive games in the month of December earned him a spot on WhoScored.com Team of the Month for December 2019. On 22 July 2020, ahead of the final game of the 2019–20 season, Rafael was announced as the clubs player of the season.