On the evening of March 4, 1959, on the way to meet a lawyer friend while crossing the Nossa Senhora de Copacabana Avenue, in Rio de Janeiro, he was run over by a State's motor vehicle and he got a broken skull, going into a coma. He died on March 16, 1959, around 5:00 pm, in the Hospital Sousa Dias. In 1965 his remains were transferred to Lisbon and since 11 November 1966 they are buried in the Alto de São João cemetery. By that time, his widow also sent Botto's archives to a Portuguese relative of hers who later donated them to Lisbon's Biblioteca Nacional in 1989.