[1][2] 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.

Respected for his "tact and sagacity", Thayer's involvement was often sought to settle ecclesiastical disputes across the state of Massachusetts.

[2] For a number of years, Thayer was involved in a dispute with James G. Carter, then-Deacon of Thayer's congregation and later a member of the Massachusetts House of Representatives, over the latter's refusal to return funds donated toward the establishment of an instructional academy that failed to materialise.

Thayer publicly denounced Carter's actions and called on him to reimburse donors of the failed project.