Ferneyhough was born in Coventry and received formal musical training at the Birmingham School of Music and the Royal Academy of Music from 1966–67. His teachers there included Lennox Berkeley, a respected teacher though a conservative figure who preferred the works of French impressionism to the internationalist avant garde. Ferneyhough was awarded the Mendelssohn Scholarship in 1968 and moved to mainland Europe to study with Ton de Leeuw in Amsterdam, and later with Klaus Huber in Basel. Between 1973 and 1986 he taught composition at the Hochschule für Musik Freiburg, Germany.
His profile rose in the middle of the 1970s, as the Royan Festival of 1974 saw the premiere of Cassandra's Dream Song, the first of several pieces for solo flute, as well as Missa Brevis, written for 12 singers. In 1975, performances of his work for large ensemble Transit and Time and Motion Study III were given; the former piece being awarded a Koussevitzky prize, the latter performed at the prestigious Donaueschingen festival. In many of these events he was twinned with fellow British composer, Michael Finnissy, whom he became friends with during his student days. In 1984 he was given the title Chevalier de l'Ordre des Arts et des Lettres.
Between 1987 and 1999 he was Professor of Music at the[University of California at San Diego. As of 1999, he is William H. Bonsall Professor in Music at Stanford University. For the 2007–08 academic year, he was appointed Visiting Professor at the Harvard University Department of Music. Between 1978 and 1994 Ferneyhough was a composition lecturer at the Darmstädter Ferienkurse and, since 1990, has directed an annual mastercourse at the Fondation Royaumont in France.
In 2007, Ferneyhough received the Ernst von Siemens Music Prize for lifetime achievement, which includes a 200,000 Euro cash award.
In 2009 he was appointed foreign member of the Royal Swedish Academy of Music.
Ferneyhough's initial forays into composition were met with little sympathy in England. His submission of Coloratura to the Society for the Promotion of New Music (SPNM) in 1966 was returned, with a suggestion that the oboe part should be scored for clarinet. However, whilst Ferneyhough did find it hard, one source of support came from Hans Swarsenski who saw the same thing happen to Cornelius Cardew; Cardew enjoyed a prestigious continental reputation, but a poor one in his homeland. Swarsenski said of Ferneyhough: 'I've taken on an English composer who is I think is enormously talented. If this doesn't work, this is the last time'. Ferneyhough continued to struggle, but the aforementioned Royan festival marked a breakthrough for Ferneyhough's career.
From here, Ferneyhough became closely associated with the so-called New Complexity school of composition (indeed, he is often referred to as the "Father of New Complexity"), characterized by its extension of the modernist tendency towards formalization (particularly as in integral serialism). Ferneyhough's actual compositional approach, however, rejects serialism and other "generative" methods of composing; he prefers instead to use systems only to create material and formal constraints, while their realisation appears to be more spontaneous. A recurring feature of his works is the use of rhythmic tuplet notation, and layered polyrhythms. Unlike many more formally-inclined composers, Ferneyhough often speaks of his music as being about creating energy and excitement rather than embodying an abstract schema. His pieces rarely use 12-note rows, but do include microtones and frequent use of glissando.
His scores make huge technical demands on performers; sometimes, as in the case of Unity Capsule for solo flute, creating parts that are so detailed they are likely impossible to realize completely. The compositions have, however, attracted a number of advocates, among them the Arditti Quartet, ELISION Ensemble, the members of the Nieuw Ensemble, Ensemble Contrechamps, Ensemble Exposé, Armand Angster, James Avery, Massimiliano Damerini, Arne DeForce, Friedrich Gauwerky, Nicolas Hodges, Mark Knoop, Geoffrey Morris, Ian Pace, Carl Rosman, Harry Spaarnay, and EXAUDI Vocal Ensemble.
Recently, he has started writing works which allude to past composers; his Dum transisset are based on Elizabethan composer Christopher Tye's works for viol. In addition, the fourth string quartet references Schönberg. One of his latest works, an opera, Shadowtime, with a libretto by Charles Bernstein, and based on the life of the German philosopher Walter Benjamin, was premiered in Munich on 25 May 2004, and recorded in 2005 for CD release in 2006. As is usual for Ferneyhough's works, the opera received mixed reviews. In addition, the production was picketed by a group called Militant Esthetix over the treatment of and association with Walter Benjamin, amongst other things.
Ferneyhough uses the software packages OpenMusic, PatchWork (PW) and the PatchWork successor PWGL.