O’Donoghue is born to Irish parents and grows up in the Hans Town area of Chelsea. He is the son of John O’Donoghue, a bricklayer from Kilworth, County Cork, and Bridget Griffin, who is from County Tipperary. He is the third of nine children, and has four brothers, Thomas, John, James, and Edmund, and four sisters, Mary, Ellen, Katherine, and Agnes. He is first an upholsterer‘s apprentice from the age of sixteen before becoming a journalist and author.
O’Donoghue attends a Catholic school and furthers his education at the British Museum. He begins his journalistic work by writing for the Dublin papers upon subjects relating to Irish music, art, and literature. A founder-member of the Irish Literary Society in London, he is also vice president of the National Literary Society, Dublin, and the compiler of a biographical dictionary, The Poets of Ireland (1891–93; revised edition, 1912), with entries on 2,000 authors. His published works also include Irish Poetry of the Nineteenth Century (1894), Humor of Ireland (1894), List of 1300 Irish Artists (1894), The Life and Writings of James Clarence Mangan (1897), Bibliographical Catalogue of Collections of Irish Music (1899), and Geographical Distribution of Irish Ability (1906).
O’Donoghue publishes an edition of James Fintan Lalor‘s writings (1895) and an edition of William Carleton‘s Traits and Stories of the Irish Peasantry (four volumes, 1896–97). He edits the works of Samuel Lover (six volumes, 1898–99) and the prose works (1903) and poems (1904) of James Clarence Mangan. He writes biographies on William Carleton (1896), Richard Pockrich (1899), and Robert Emmet (1902).
In 1896 O’Donoghue moves to Dublin. In 1909 he becomes librarian of University College Dublin. He is co-editor of Catalogue of the Gilbert Library (in Dublin; 1918). William Butler Yeats writes of him in his Autobiographies of William Butler Yeats (1938).