Thayer spent his boyhood in Vermont and New Hampshire, where he developed an early interest in wildlife. While at the Chauncy Hall School in Boston from 1864 to 1867, he received some instruction in art from Henry Morse. He executed animal portraits on the side. His move to Brooklyn, New York, in 1867 enabled him to study with J. B. Whittaker at the Brooklyn Academy of Design, and at the Academy school, where he was enrolled in the antique class from 1870 to 1874, and the life class from 1871 to 1873. He married Kate Bloede in 1875, and the two left for Paris where Thayer worked for four years at the Ecole des Beaux-Arts under Henri Lehmann and Jean-L‚on G‚r"me.
After his return to Brooklyn in 1879, Thayer spent the next two decades living variously in New York, Massachusetts, Connecticut, and New Hampshire. He was active in the Society of American Artists, serving as its vice president and president in 1883 and 1884. Election to the Academy followed his receipt of the Clarke Prize in its annual exhibition of 1898. By then, he had given up his earlier mode of cattle scenes and landscapes, opting instead for idealized figural works which often depicted his family and friends. (He remarried in 1891 shortly after the death of his first wife.)
Thayer had designed and built a summer home on property given him in Dublin in 1888. As of 1901 he lived there year-round, adopting an insular and eccentric lifestyle defined by phobias and an intense devotion to his natural surroundings. Much of the next few years were dedicated to advancing his theories on protective coloration, published in 1909 in his book, Concealing Coloration in the Animal Kingdom. He did continue to exhibit with the Academy, and in the 1915 annual, received the Saltus Medal. Late in life, he was supported by two wealthy patrons, Charles Lang Freer and John Gellatly.
