He was born in Liverpool, England, and sang in his high school choir. He played the violin and was awarded a scholarship. While studying chemistry and physics at Liverpool University, he studied voice with Austen Carnegie. He was a member of staff at Acton Technical College until 1957 and played a part in events leading to the formation of Brunel University. He was a Vicar Choral at St Paul's Cathedral 1961-62.
He made his operatic debut in Debussy's Pelléas et Mélisande at the Glyndebourne Festival in 1961, was a member of the English Opera Group from 1964 - 1976, and was thus prominent in performing and recording the operatic and vocal works of Benjamin Britten. These included the première performances of Canticle IV: Journey of the Magi and Death in Venice. The latter part was written specially for him, and involves multiple roles as antagonist to the character of Gustav von Aschenbach. In 1977 he created the role of Lev in Sir Michael Tippett's The Ice Break at Covent Garden.
He appears regularly with major orchestras and opera companies throughout the world and has a vast discography. Notable recordings include many of Britten's works and Mahler's Eighth Symphony under Sir Georg Solti on Decca, and Vaughan Williams' vocal works under Sir David Willcocks and the Choir of King's College, Cambridge for EMI. He also sang in the premiere recording of Delius's Requiem in 1968, under Meredith Davies, shortly after a rare live performance (only the work's fifth performance in 62 years) at the Albert Hall with the same forces. Among his early recordings for Saga of British songs is the first complete version (including the Epilogue) of Vaughan Williams's Songs of Travel. He was also the soloist in the first recording of Tippett's The Vision of St. Augustine under the composer's baton in 1971.
In 1975, John Shirley-Quirk was made a Commander of the Order of the British Empire (CBE).
He is currently on the faculty of the Peabody Conservatory of Music in Baltimore, MD.
Shirley-Quirk was married to Patricia ("Pat") Hastings, who died in 1981, then oboist Sara Watkins, who died in 1997. In 2009 he married cellist Teresa Perez.