Born in London, Hughes was educated at Archbishop Tenison's Grammar School, and entered the School of Design, Somerset House, London in 1846, studying under Alfred Stevens. In 1847 he won an art studentship at the Royal Academy Schools, exhibiting his first picture, Musidora, at the Academy two years later.
Although a Pre-Raphaelite sympathiser and intimate of their circle, Hughes was never a member of the group. He converted to Pre-Raphaelitism in 1850 after reading the Pre-Raphaelite magazine The Germ; in the same year he met William Holman Hunt, D.G. Rossetti and Ford Madox Brown. He exhibited his first Pre-Raphaelite painting, Ophelia (Manchester City Art Gallery), in 1852, and met Millais that year. He produced some of his best-known Pre-Raphaelite works during the 1850s, including April Love, 1855-6 (Tate Gallery N02476) and The Long Engagement, c.1854-9 (Birmingham Museum and Art Gallery). From about 1852 to 1858 he shared a studio with the sculptor Alexander Munro. He married Tryphena Foord in 1855, eventually having five children. In 1855 he also began a successful career as an illustrator, becoming associated particularly with the works of Thomas Hughes, George Macdonald and Christina Rossetti. He devoted much of the subsequent two decades to illustrating. He was one of the contributors to the Oxford Union decorations in 1857. He moved from London in 1858 and in 1862 made a short visit to Italy. He exhibited for the last time at the Royal Academy in 1908. He died at Kew, near London. A sale of his works took place at Christie's in 1921.
Retrospective exhibitions of Hughes's work were held by the Fine Arts Society in 1900, Rembrandt Galleries in 1904, Walker Galleries (memorial exhibition) in 1916, and the National Museum of Wales, Cardiff and Leighton House, London in 1971.