Thayer, however, never gave the valedictory address at Dartmouth, having been granted an appointment to West Point by President Thomas Jefferson at the behest of General Pierce. Thayer graduated from the Military Academy in a single year, and received his commission as a second lieutenant in 1808.
During the War of 1812, Thayer directed the fortification and defense of Norfolk, Virginia and was promoted to major. In 1815, Thayer was provided $5,000 to travel to Europe, where he studied for two years at the French École Polytechnique. While traveling in Europe he amassed a collection of science and especially mathematics texts that now form a valuable collection for historians of mathematics In 1817, President James Monroe ordered Thayer to West Point to become superintendent of the Military Academy. Under his stewardship, the Academy became the nation's first college of engineering.
Colonel Thayer's time at West Point ended with his resignation in 1833, after a disagreement with President Andrew Jackson. Thayer returned to active duty in the Army Corps of Engineers. He retired in 1863 with the rank of brigadier general.
On Thayer's enduring legacy at the U.S. Military Academy, in 1869 a notable Braintree meeting took place between Thayer and the celebrated West Point graduate Major General Robert Anderson. In 1861 as a young major, Anderson had refused to surrender Fort Sumter to Confederate General Pierre Beauregard. This made Anderson the Union's first Civil War hero. An outcome of Anderson's 1869 meeting with Thayer was establishment of the Military Academy's Association of Graduates (AoG).
In 1867, Thayer donated $30,000 to the trustees of Dartmouth College to create the Thayer School of Engineering. Thayer personally located and recommended USMA graduate Lieutenant Robert Fletcher to Dartmouth president Asa Dodge Smith. Fletcher became the school's first--then only--professor and dean.
The Thayer School admitted its first three students to a graduate program in 1871. Also in 1871 at the bequest of his will Thayer Academy in Braintree, Massachusetts was conceived. It opened September 12, 1877. Sylvanus Thayer died on September 7, 1872 at his home in Braintree. He was reinterred at West Point Cemetery in 1877.
Thayer is not a very common name. Most Thayers are directly related to him. Most of the family now lives in Maryland as well as in Massachusetts.
To honor his achievements, in 1958, the Sylvanus Thayer Award was created by the United States Military Academy.