He entered Dartmouth College in 1803 but left in 1807 to attend the U. S. Military Academy at West Point. He graduated in 1808.
He was commissioned in the Corps of Engineers, and served in the War of 1812. In 1815 he was breveted a major and ordered to study European methods of educating military engineers so that he might help rescue West Point from incipient decay. The academy had a reputation for laxity in discipline and academic standards and suffered from uncertainty about whether to stress civilian or military studies. After a year at the French École Polytechnique studying the curriculum and gathering a library, Thayer became superintendent at West Point in 1817. He accomplished sweeping reforms, setting new standards for admission, establishing minimum levels of academic proficiency, and creating a system to measure cadet progress. A commandant of cadets was appointed to regulate discipline and the military curriculum. Thayer established a board of visitors to inspect the academy annually to recommend adjustments in curriculum. He also established an academic board of faculty and administrators to develop academic policy. Because West Point was required to provide professional officers for the Army, military subjects dominated the program. Thayer believed that the arts and sciences were important, as he wanted graduates to discharge the civilian offices of life with distinction. Courses in English and French, the natural and social sciences, mathematics, and ethics became staples. Refinements increased the civilian applications of West Point's curriculum. By 1831 the military engineering course was designated "civil engineering" and had lost most of its military overtones, encompassing the construction of "buildings and arches, canals, bridges, and other public works. " Some graduates applied this in building the communications network to support America's developing industrial system. Suspicion that the academy was an incubator of a military aristocracy led to tensions between Thayer and President Andrew Jackson's administration. Thayer was reassigned in 1833 as a colonel to supervise the construction of fortifications and harbor improvements in Massachusetts and Maine. He became commander of the Corps of Engineers in 1857 but took a sick leave in the next year. Thayer retired in 1863 as a brigadier general. In 1867 he endowed the Thayer School of Engineering at Dartmouth and spent his last years arranging its curriculum. He died in Braintree on September 7, 1872.