Born in Lincolnshire, the son of very indigent parents, Stubbe had been carried by them into Ireland, whither they had migrated for a livelihood. In 1641, on the outbreak of the Irish Rebellion, his mother had brought him and another child back, landing in Liverpool and walking with them on foot all the way to London. Supporting them there with the utmost difficulty by her needle, she yet contrived to send Henry to Westminster School; where Busby, the head-master, finding him excessively clever, did what he could for him. One day Sir Henry Vane, visiting the school, had the boy introduced to him by Busby; and from that moment Stubbe recognised Vane as the man to whom he was most indebted in the world. By Vane's interest he was admitted in 1649 into Christ Church, Oxford, where he remained till 1653, when he took his B.A. degree. Never had there been in the college an undergraduate at once so remarkable for scholarship, and so pragmatical, forward, and unruly in conduct. He was "often kicked and beaten," and once "whipt in the public refectory." It was in this time of his undergraduateship (1651) that he published his first book, entitled Horae Subsecivae, and consisting of translations of Jonah and other parts of the Old Testament, and of Latin epigrams by Randolph and others, into Greek. From 1653 to 1655 he had been with the English army in Scotland; and after his return he had published two more volumes of Latin and Greek verse. Having graduated M.A. in the end of 1656, he was appointed, in 1657, by Owen's influence, under-keeper of the Bodleian Library; and it was in a series of writings published by him while he held this post that he had revealed himself most characteristically. Admiring and knowing Hobbes, he had flung himself ferociously, in 1657 and 1658, into the controversy between that philosopher and Dr. Wallis, publishing two pamphlets against Wallis and heading an opposition to him in the University; besides which he had published, in 1659 or the beginning of 1600, some six or seven pamphlets on the political questions then in agitation. Originally a kind of Independent and Republican of the Vanist School, Stubbe still appeared in these writings as a strenuous Republican and antagonist of the Royalist, but with much in him of the extreme free-thinker, advocating "a democracy of Independents, Anabaptists, Fifth-Monarchy men, and Quakers," and assailing the Established Clergy. To a considerable extent his theories in Church and State just before the Restoration seem to have agreed with Milton's. But, after the Restoration, Stubbe, who had meanwhile lost his under-librarianship of the Bodleian, and gone to practise physic in Stratford-on-Avon, veered round fast enough. Having received confirmation by his diocesan Dr. Morely, he reannounced himself thus: — "I have joined myself to the Church of England, not only on account of its being publicly imposed (which in things indifferent is no small consideration, as I learnt from the Scottish transactions at Perth), but because it is the least defining, and consequently the most comprehensive and fitting to be national." Henceforth, accordingly, though pugnacious as ever, and a Hobbist or free-thinker at heart, with an undying affection for Vane, he was to be known as Stubbe metamorphosed. After trying the West Indies, he was to return to Stratford-on-Avon, resume medical practise there, remove subsequently to Warwick and to Bath in the same practise, and publish a great many writings, chiefly scientific and medical, but some of them political. His end, like his life, was tragi-comic. He was drowned in crossing a shallow stream near Bath, on the 12th of July, 1676, "his head being then intoxicated with bibing, but more with talking and snuffing of powder," says the punctual Wood, whose character of him, all in all, is that he was "the most noted person of his age that these late times have produced."