Her first published works were illustrations and illuminations for an 1861 edition of Ferguson's poem The Cromlech at Howth; the title page conflated parts of the illuminations on two pages of the Book of Kells. In the 1870s she edited Dunraven's Notes on Irish Architecture (3 volumes, 1875–1877) after the author's death in 1871. Her Early Christian Art In Ireland (1887, 2nd edition 1911) was well regarded, and if reviewer Oscar Wilde was unmoved by Stokes' prose, he praised her illustrations. She produced two works on early medieval Irish saints in Europe, Six Months in the Apennines (1892) and Three Months in The Forest of France (1895). Her High Crosses of Ireland was incomplete at her death.