He was educated at Balliol College, Oxford; he obtained a First in Classical Moderations in 1888 and a First in Literae Humaniores ('Greats', a combination of philosophy and ancient history) in 1890.
For Oxford University Press, Stuart Jones edited Thucydides' Historiae, the history of the Peloponnesian War, in two volumes.
Stuart Jones began in 1911 the revision of A Greek-English Lexicon, the standard dictionary of ancient Greek, with the assistance of Roderick McKenzie.
In a preface to the revision, the Press described Stuart Jones in these terms: Sir Henry was the ideal Editor; his wide range of knowledge and his exact scholarship, his persistent devotion to his task even in periods of ill health, his tactful assiduity in consulting experts and his skill in co-ordinating their results, gave the work at once its consistency and its elasticity.
His tenure in Wales would prove to be an enthusiastic one: during his time there, he learned the Welsh language and served on the committees of a number of Welsh institutions, including the council of St David's College, Lampeter, as well as Trinity College, Carmarthen, and the National Library of Wales.