Bowen was born at Woolaston in Gloucestershire — his father, Rev. Christopher Bowen, originally of Hollymount, County Mayo, being then curate of the parish and his mother, Catherine Steele (1807/8–1902) his younger brother was Edward Ernest Bowen, a long - serving Harrow schoolmaster. He was educated at Lille in France, Blackheath and Rugby schools, leaving the latter in 1853 having won a scholarship to Balliol College, Oxford.

There he made good his earlier academic promise, winning the principal classical scholarships and prizes of his time. He was elected a Fellow of Balliol in 1857 while an undergraduate and became President of the Oxford Union in 1858.