Hughes was born and brought up in Belfast, Ireland, but completed his formal music education at the Royal College of Music, London, where he studied with Charles Villiers Stanford and Charles Wood, graduating in 1901. Subsequently, he worked as a music critic, notably for The Daily Telegraph from 1911 to 1932.
Described as having an "ardent and self-confident manner", Hughes is first heard of in an Irish musical capacity (beyond being honorary organist at St Peter's Church on Antrim Road at the age of fourteen) collecting traditional airs and transcribing folksongs in North Donegal in August 1903 with his brother Fred, F.J. Bigger, and John Campbell. Dedicated to seeking out and recording such ancient melodies as were yet to be found in the more remote glens and valleys of Ulster, he produced Songs of Uladh (1904) with Joseph Campbell, illustrated by his brother John and paid for by Bigger. Throughout his career, he collected and arranged hundreds of traditional melodies and published many of them in his own unique arrangements. Three of his best-known works are the celebrated songs, My Lagan Love, She Moved Through the Fair, and Down by the Salley Gardens, which were published as part of his four collections of Irish Country Songs, his key achievement. These were written in collaborations with the poets Joseph Campbell and Padraic Colum, and Yeats himself. A dispute with Hamilton Harty over copyright on My Lagan Love was pursued on Bigger's advice, but failed.
Married to Lillian Florence (known as Meena) Meacham and Suzanne McKernan, Herbert had three children: Patrick (known professionally as Spike Hughes), Angela and Helena. He died in Brighton, England, at the relatively early age of fifty-four.
Hughes had a unique approach to arranging Irish traditional music. He called upon the influence of the French impressionist Claude Debussy in his approach to harmony: "Musical art is gradually releasing itself from the tyranny of the tempered scale. [...] and if we examine the work of the modern French school, notably that of M. Claude Debussy, it will be seen that the tendency is to break the bonds of this old slave-driver and return to the freedom of primitive scales." He regarded arrangements as an independent art form on an equal level with original composition: "[...] under his [i.e. the arranger's] hands it is definitively transmuted into an art-song, an art-song of its own generation.". Hughes's folksong arrangements have been sung all across the English-speaking world; John McCormack and Kathleen Ferrier were the first to record them on gramophone records.
An admirer of James Joyce's poetry, Hughes in 1933 edited The Joyce-Book, a volume of settings of Joyce's poetry, with 13 pieces by 13 composers including, besides Hughes himself, Arnold Bax, Arnold Bliss, Herbert Howells, John Ireland, and non-British composers such as George Antheil, Edgardo Carducci, and Albert Roussel. The large-format, blue-cloth covered volume has since become a collector's item.
Hughes also composed a limited amount of original chamber music and some scores for the stage (like And So to Bed by John Bernard Fagan) and film. Hughes and John Robert Monsell also created songs for a musical version of Richard Brinsley Sheridan's The Rivals called Rivals!, which was staged at the Kingsway Theatre in London in September 1935 by Vladimir Rosing.