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. Also succeeding Davison, he became editor of the Musical World in 1886 and actuated a more musically progressive attitude. He fell ill in the summer of 1888 and died of cancer on 19 January 1889.
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.
- 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
- Hughes, Meirion (2002). The English Musical Renaissance and the Press 1850–1914: Watchmen of Music. Aldershot: Ashgate. pp. 27–28.
- 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.