Fernández studied at the Instituto Nacional de Música with Francisco Braga, Frederico Nascimento, and Henrique Oswald.

In 1923, Nascimento was taken seriously ill, and Fernández was designated his temporary substitute in the chair of upper-level harmony, an appointment which became permanent two years later.

In 1930 Fernández composed the three-movement suite Reisado do Pastoreio, the last movement of which, "Batuque" (an Afro-Brazilian folk dance), became very popular.

He composed a three-act opera, Malazarte (1931–33), to a libretto by José Pereira Graça Aranha, who adapted it from his own play of the same title.

Malazarte is a nationalist work in both its subject matter and its musical content, and is considered the first successful Brazilian opera of this type.