In 1672 Hoar went again to Massachusetts to preach, by invitation, at the Old South Church, Boston. He brought a letter, dated 5 February 1672, addressed to the magistrates and ministers in Massachusetts Bay by thirteen nonconformist ministers in and around London, friends of the colony and agents in raising funds for a new college building, who strongly recommended Hoar for the post of president of Harvard as successor to Charles Chauncy, who died 19 February 1672. The general court voted an increase of salary on the condition that Hoar was elected. He was accordingly chosen, to the disappointment of Urian Oakes, who was widely regarded as Chauncy's legitimate successor. Hoar was immediately elected and installed as President of Harvard on December 10, 1672; a position he held until he resigned on March 15, 1675. Hoar had high ambitions for Harvard as research centre, as he wrote to Robert Boyle at this time. He modernized technical education by introducing a garden and orchard, a workshop, and a chemical laboratory to Harvard. He was the first president of Harvard College who was also a graduate of it; but he was not well liked by his students or the people of Massachusetts, in part because of his radical religious views. The facts of his time in office remain obscure. Samuel Sewall was educated at Harvard by Hoar, one of only three students to graduate from Harvard in 1673. He was also one of the few to come to Hoar's defense in 1674 or 1675, just before Hoar was forced to resign. Some members of the corporation had combined against him, with the result that all the students, with the exception of three, had left. Sewall later argued that "the causes of the lowness of the Colledge were external as well as internal." Daniel Munro Wilson wrote
At all events the students fell away from the president, and 'set themselves to Travestie whatever he did and said, and aggravate everything in his behavior disagreeable to them, with a design to make him Odious'.
'Index Biblicus: or, the Historical Books of the Holy Scripture abridged. With each book, chapter, and sum of diverse matter distinguished, and a chronology to every eminent epocha of time superadded. With an Harmony of the Four Evangelists and a table thereunto, &c.' , London, 1668. It was afterwards reissued as 'Index Biblicus Multijugus: or, a Table to the Holy Scripture. The second edition, &c.' , London, 1672.
'The First Catalogue of Members of Harvard College,' 1674. The only copy known was found in 1842 by James Savage in the State Paper Office in London, and was printed in the 'Proceedings' of the Massachusetts Historical Society for October 1864, a few copies with a title-page being issued separately.
'The Sting of Death and Death Unstung, delivered in two Sermons, preached on the occasion of the death of the Lady Mildmay,' Boston , 1680, published by Hoar's nephew, Josiah Flint.
