As Brigadier General he was Head of the Special Forces Detachment and Commander of the Ninth Armored Division.
In 1981 he was Commander General of the Army and as such was responsible for the operations of the Cordillera del Condor, acting at the Paquisha point in the confrontation with Ecuador.
In June 1981, while undertaking a Command visit, General Hoyos Rubio was killed in an air accident.
Rubio, who had been one of the conspirators in the de Velasco coup, implored officials to never again stop aspiring towards saving the country.
In 2007 the "Major General Rafael Hoyos Rubio" Military College was founded in the city of Cajamarca.