Thayer had been admitted to the Massachusetts Bar Association, but never practiced law. He was an alderman in Worcester from 1852 to 1853. He was elected to the Massachusetts House of Representatives in 1853 and 1854. While there he devised and obtained a charter for the New England Emigrant Aid Company. The purpose of the Company was to finance people from New England to settle in Kansas. Under the popular sovereignty doctrine they could vote it free of slavery if and when it became a state. Thayer received a percentage of all the money collected by the Company.