Hueffer was born in Münster, Germany, on 22 May 1845. He studied modern philology and music in London, Paris, Berlin, and Leipzig, and earned a Ph.D. in 1869 from the University of Göttingen for a critical edition of the works of Guillem de Cabestant, a 12th-century troubadour.
Following his studies, he moved to London in 1869 as a writer on music, and from 1878 worked as music critic for The Times, succeeding James William Davison. He wrote a number of books on music, especially on music history and biography; edited the Great Musicians series for Novello & Co; and translated the correspondence of Richard Wagner and Franz Liszt to English. He also wrote the libretti for several English operas: Alexander Mackenzie's Colomba and The Troubadour, and Frederic Hymen Cowen's Sleeping Beauty.
Hueffer's wife, Catherine Madox Brown, was an artist and model associated with the Pre-Raphaelites. Their sons, Ford Madox Hueffer (better known as Ford Madox Ford) and Oliver Madox Hueffer, were writers.
Hueffer died on 19 January 1889.
- Richard Wagner and the Music of the Future (1874) (reissued by Cambridge University Press, 2009; ISBN 978-1-108-00474-9) (Google Books)
- The Troubadours: A History of Provençal Life and Literature in the Middle Ages (1878) (Internet Archive)
- Musical Studies: A Series of Contributions, a collection of his articles from The Times and Fortnightly Review (1880) (reissued by Cambridge University Press, 2009; ISBN 978-1-108-00473-2) (Internet Archive)
- Wagner, in the Great Musicians series (1881) (reissued by Cambridge University Press, 2009; ISBN 978-1-108-00475-6) (Internet Archive)
- Italian and Other Studies (1883) (Google Books)
- Half a Century of Music in England: Essays Towards a History (1889; 2nd ed. 1898) (reissued by Cambridge University Press, 2009; ISBN 978-1-108-00472-5) (Internet Archive)
- Correspondence of Wagner and Liszt (1889; as translator) (reissued by Cambridge University Press, 2009; ISBN 978-1-108-00474-9) (Project Gutenberg: vol. 1; vol. 2)
- Oxford Dictionary of National Biography; Baker's gives a date of birth of 23 May 1843
- J. A. F. Maitland and John Warrack (2004). "Hueffer, Francis". Oxford Dictionary of National Biography. 28. p. 597.
- Theodore Baker and Alfred Remy, ed. (1919). "Hueffer, Francis". Baker's Biographical Dictionary of Musicians (3rd ed.). pp. 419–420.