Francis Samuel Thayer (September 11, 1822 in Dummerston, Windham County, Vermont – November 26, 1880 in Colorado Springs, El Paso County, Colorado) was an American merchant and politician from New York.
Then he attended Cambridge Academy for four months, and during the winter of 1841–42 taught school in North Bennington, Vermont.
After five years, he was made a partner, and engaged extensively in the flour and milling business.
At the New York state election, 1873, he ran on the Republican ticket for Secretary of State of New York, but was defeated by Democrat Diedrich Willers, Jr. Thayer was Auditor of the Canal Department from April 15, 1874, to December 28, 1875, when he was suspended, in connection with the canal investigation.
He went to Colorado Springs, hoping to find relief from his asthma, and died there.