Born and raised in rural Massachusetts, Cephas Giovanni Thompson received his earliest artistic training from his father, Cephas Thompson, a self-taught portraitist. According to Henry T. Tuckerman he moved to Boston around 1829 where, under the instruction of David Claypoole Johnston, he began drawing the casts from the antique owned by the Boston Athenaeum. Thompson subsequently worked as a portraitist in Providence, Rhode Island, and in 1837 he moved to New York City. During the following ten years his paintings were frequently shown at the Academy. In 1842 he married Mary Gouverneur Ogden, daughter of a prominent merchant, and he soon became closely associated with New York's literati. In 1847 Thompson returned to Massachusetts where he spent several years working in Boston and New Bedford prior to his departure for Rome in 1852. Thompson spent seven years in Rome studying the old masters. While he continued to work primarily as a portraitist during this period, he also began painting allegorical and religious subjects.
Thompson's understanding of the old masters was praised in both James Jackson Jarves' The Art-Idea and Nathaniel Hawthorne's The Marble Fawn and thus his return to America in 1859 was met with great enthusiasm. He spent his remaining career working in New York City and found a ready demand for both his portraits and his Italian genre scenes.
At the Academy's Council Meeting of January 9, 1888, he was remembered as "a gentleman of the Old School -- an Artist of sincere and worthy aspiration, always striving for the utmost -- and a man of refinement and culture and of most gentle and kindly manners."