Barraqué stated that he wrote about 30 works before those that he eventually acknowledged; as far as is known they were destroyed by him. They included a Nocturne and Mouvement lent for piano, at least three piano sonatas, a sonata for unaccompanied violin, and a Symphony in C sharp minor. The presumably fourth, but un-numbered Piano Sonata, for which he gave the date 1952, was his earliest acknowledged work. Barraqué then produced his only electronic piece, the musique concrète Etude (1954), made at Pierre Schaeffer's studio. Subsequently he planned a large-scale cycle of pieces, La Mort de Virgile, based on Hermann Broch's novel The Death of Virgil, a book which Barraqué's friend and sometime lover Michel Foucault recommended to him. This cycle, along with other pieces deriving from it or acting as commentaries upon it, he envisaged as his principal lifelong creative project. Following the scheme of the novel, it was to be divided into four sub-cycles: 'Water (The Arrival)', 'Fire (The Descent)', 'Earth (The Expectancy)' and 'Air (The Return)'. Most of Barraqué's creative efforts went into the works which were to take their place in 'Fire (The Descent)', which - to give an idea of the projected scope of the whole design - was to have consisted of thirteen works. Before his death he completed two of the projected parts: Chant aprés chant (1966), and Le temps restitué (1957/68). Fragments of some of the other parts exist.
Barraqué also wrote ... au dela du hasard (1959) for three female voices and ensemble, and a concerto for clarinet, vibraphone and ensemble in 1968, which are related to The Death of Virgil, but not actually part of that cycle. (... au dela du hasard is described as a commentary on Affranchi du hasard, which was to have been the eleventh piece of 'Fire (The Descent)' but was not actually composed.) The only other extant piece by Barraqué is Séquence (195556), a setting of Nietzsche for soprano and ensemble which is partly a re-working of three songs for soprano and piano from the early fifties.
Barraqué's use of tone rows in his work is quite distinctive. Rather than using a single tone row for an entire piece, as Anton Webern did, or using a number of related rows in one work, as Alban Berg or Arnold Schoenberg sometimes did, Barraqué starts by using one row, and then subtly alters it to get a second. This second row is then used for a while before being slightly altered again to make a third. This process continues throughout the work. He called this technique "proliferating series".
Harry Halbreich has written that "Barraqué's whole work is marked by terrible despair, lightened by no religious or ideological faith, and entirely dominated by the great shadow of Death". In 1998 the record company CPO issued his entire output on CD, in performances by the Austrian ensemble Klangforum Wien.
The major reference work on his music in English is a biography entitled The Sea on Fire by the British music critic Paul Griffiths (2003). In German, Heribert Henrich's book of 1997 is its complement. His music is now published by the German firm of Bärenreiter.