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The multi-sport Club de Regatas Botafogo (Botafogo Rowing Club), abbreviated as C.R. Botafogo, was founded in 1894. The club's basketball section was founded in 1933, and were finalists of the Rio de Janeiro State Championship, in 1934 and 1937. The multi-sport club Botafogo Football Club, abbreviated as Botafogo F.C., was founded in 1904. Its basketball section won the Rio de Janeiro State Championship in 1939 and 1942.

Basketball played a major role in the development of Botafogo F.R.'s multi-sports athletic club. In 1942, a basketball game was played between the two sports clubs of the Botafogo neighborhood, C.R. Botafogo and Botafogo F.C., respectively. During the game, just after halftime, Armando Albano, a player of Botafogo F.C., died on the court, after suffering a heart attack. In his honor, the presidents of each club decided to merge their clubs, and become Botafogo de Futebol e Regatas (Botafogo Football and Rowing), abbreviated as Botafogo F.R. The club also took a new flag and a new crest, mixing both club's originals. After that, Botafogo F.R.'s basketball club won several local Rio de Janeiro State Championships, including the three-peat of 1943, 1944, and 1945.

Botafogo F.R. also won the Brazilian Cup (Brazilian Championship) title in 1967, and became the first and only club from Rio to win the top-tier level Brazilian league. Another club from Rio did not do so until 2000. They also competed in the 1968 edition of the FIBA Intercontinental Cup. At the beginning of the 2000s decade, the club's basketball department became amateur, and only became professional again in 2015.

In the 2017 season, Botafogo F.R. played in the Brazilian Gold League, the second-tier level of Brazilian pro club basketball. The club finished the regular season in first place, and went on to win the league title. They beat Blumenau in the playoffs, and then won the league's finals, after beating AAB Joinville in the 5th and decisive game, at home, by a score of 90–68. The team's main star, Jamaal Smith, was named the league's Finals MVP, after a great performance during the series.

In the 2018–19 NBB season, with Léo Figueiró already as head coach, the team reached the semifinals, losing to Flamengo Basketball that would go to win the league's title. Coach Léo Figueiró was named NBB's Coach of the Year. With this campaign, Botafogo finished 4th and secured a place at the Liga Sudamericana de Básquetbol's next season.

At the beginning of the 2019–20 season, the team debuted at the Liga Sudamericana de Básquetbol, in a group hosted in San Andres, Colombia, that had the home team Warriors de San Andrés, Nacional de Montevideo and Salta Basket. After finishing 2–1, the team advanced to the semifinals stage. The next stage was played in La Banda, and Botafogo faced, once again, Salta and Nacional, and the home team Ciclista Olímpico. At the first game, Botafogo beat Salta 62–61 with a buzzer-beater shot from Arthur Bernardi. The next day the team beat Nacional by a 10 points margin and, at the final and decisive game, Jamaal Smith put on a show and helped Botafogo come from a 17 point deficit against Ciclista Olímpico to advance to the Finals to face Corinthians. After losing the first game of the finals in Rio, the team counted with amazing performances of Jamaal Smith and Cauê Borges in game 2 and 3 respectively to win back to back games in São Paulo to conquer its first international trophy. The next day, a huge crowd of fans showed up to receive the players and celebrate the title at the club's Ginásio Oscar Zelaya.