Thayer graduated from Phillips Exeter Academy, then Harvard College in 1789 and was ordained junior pastor of a Congregational meeting house in Lancaster, Massachusetts on October 9, 1793. In 1789 the town of Lancaster gave him land on Main street, just south of the church, to build a permanent residence. There he built a twelve-room home. He received a Doctor of Divinity degree from Harvard in 1817. The Lancaster congregation's fifth meeting house designed by Charles Bulfinch in 1816, was built during his tenure.