At seventeen he entered Bristol Baptist College, where he showed such promise that in 1793 he was called to the church at Northampton to succeed Dr. John Ryland, who became president at Bristol.
Staughton early looked to America as his future field of labor, so when Dr. Richard Furman wrote to Dr. John Rippon of London asking him to suggest "a young man of promise and character" for South Carolina, he went supported by strong commendations. He arrived at Charleston, South Carolina, in the fall of 1793. For about a year and a half he supplied at Georgetown, South Carolina, a church soon being formed. In the summer of 1795 he went to New York, became head of an academy at Bordentown, New Jersey, and on June 17, 1797, was ordained there. Moving in 1798 to Burlington, where there was a larger academy, he organized a small Baptist church which he served as pastor. He edited several works in the classics and for his talents received the degree of Doctor of Divinity from the College of New Jersey (later Princeton). In 1811, partly on account of some internal tension over his English birth (superficially indicated by the remark of the sexton regarding a smoking stove, "There must be an Englishman in the stovepipe"), he became pastor of what was known as the Sansom Street Baptist Church, a new church in the western part of the city. In 1814 he took an active part in organizing the Triennial Convention and as its corresponding secretary until 1826, was concerned with the constant and varied problems of the foreign missionary enterprise. As the need for better-trained ministers stirred the Baptists to provide schools for their education, it was to Staughton they turned for practical leadership. So intimate was his connection with it that the educational institution could hardly be distinguished from his home. His reputation as a classical scholar was heightened by his editions of The Works of Virgil. To Which is Added a Large Variety of Botanical, Mythological, and Historical Notes, and of Edward Wetenhall's A Compendious System of Greek Grammar, both published in 1813. When the Triennial Convention took up its educational task more definitely in 1817, the incipient institution at Philadelphia was recognized as its theological department, with Staughton as principal and Irah Chase as professor of languages and Biblical literature. More definite plans for the organization of what was soon called Columbian College (later George Washington University) were adopted in 1818, but the transfer to Washington, District Of Columbia, was not made until September 1821. Staughton remained most of the time in Philadelphia until the fall of 1823, although he was installed as president on January 9, 1822, with professorial responsibilities in "General History, Belles Lettres, Rhetoric and Moral Philosophy" in the classical department, and in "Divinity and Pulpit Eloquence" in the theological department. From the beginning he visualized a university of national scope rendering service broader than that required by denominational needs, a conception which found its correlate in the world-mission ideal so dominant in Luther Rice, the chief financial agent for the college. The effective forces in the development of collegiate education during that period, however, were largely stimulated by denominational loyalties and local economic considerations, rarely entirely divorced from speculative land interests. Competing educational institutions were rapidly forming, financial complications arose, and in 1829 Staughton resigned the presidency. He was soon chosen president of Georgetown College in Kentucky. Starting for his new field, he died as he was passing through Washington.
He was a member of the Baptist Education Society of the Middle States.
He married Maria Hanson before January 1794. They had six children. A few months before his death, on August 27, 1829, he married Anna Claypoole Peale, who survived him.