Born January 19, 1823, in New Haven, Thomas Ruggles Pynchon was educated at Boston Latin School, after which he entered Trinity College (Hartford, Connecticut) in 1837. Graduating in 1841, Pynchon tutored students in Classics and lectured on Chemistry until 1847. In 1848, he became a deacon, and then priest in the Protestant Episcopal Church in 1849. In October 1854, Pynchon took a teaching position at Trinity College as the inaugural Scovill Professorship of Chemistry, named after the Scovill brothers. In 1857, he claimed the post of Librarian of the College, which he occupied at least in name until 1882.

While teaching chemistry and natural sciences at Trinity, he took one of America's first sabbatical leaves, which allowed him the time to study at Paris and Cambridge, England. He brought some chemical equipment back with him to Hartford from France, leading to a major remodel of the Chemistry Laboratory at Trinity College.

During much of the American Civil War, Pynchon served as Acting Chaplain of the college. He led the scheduled daily prayers in the morning and evening, as well as offering the Sunday service. He also served as chaplain of the college's student Missionary Society. He obtained a Doctorate in Divinity from St. Stephen's College.

Pynchon was elected President of the college in November 1874. Encouraging a policy of incremental building of the Burges architectural plan, he helped to break ground at the new Summit Campus on July 1, 1875. Still, President Pynchon faced the uneviable challenge of guiding the construction of the new campus buildings along Summit Street, as well as overseeing the last few semesters of classes taught at the "Old Campus" in downtown Hartford. Known as “Old Pynch” by some of the students, Pynchon appears not to have been a favorite among many of them. Members of several classes took to setting large bonfires, while other students called meetings and took votes to express their opinions contrary to the administration's views. He held out hope that the troublemakers on campus were largely composed of students who had started classes at the old campus and would soon graduate. He was made the Chair of Moral Philosophy in 1877.

But it was relationships between Pynchon, the faculty, and the alumni that would ultimately lead him to end his term. In October 1882, he resigned from the Presidency of Trinity, amid demands from some quarters that he resign. Yet, Pynchon stayed on at Trinity as Professor of Moral Philosophy, a post he kept until 1902. Beginning in 1888, he also held the Brownell Professorship. During the spring of 1896, he returned as Acting President of the College during a brief six-month leave granted to then-President George Williamson Smith. In 1902, his title switched to Professor Emeritus when he stopped teaching. On October 6, 1904, former professor and president Pynchon died and was buried in New Haven, Connecticut.

The History of Trinity College (1967) by Glenn Weaver, pp. 98, 115, 133, 135, 146, 171, 182-184, 188-194, 199-200, 234, 246, 256.