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He was born in Abbeyleix, Ireland. Due to the potato famine occurring in Ireland at the time, he emigrated to the United States in 1847 with his widowed mother, and they settled in Albany, New York. There, he found work as a handyman.
After studying anatomy in the office of a physician, Dr. James H. Armsby, he spent nine years as the studio boy of the sculptor, E. D. Palmer. In 1858 he moved to New York City where he opened a studio. There he shared an apartment with James Pinchot. In 1862 he was elected academician at the National Academy due to his work Rocky Mountain Trapper, a marble portrait of James "Grizzly" Adams. He visited Rome in 1868–1869, and married Maria Louisa Potter (1839–1916), daughter of Alonzo Potter, Episcopal Bishop of Pennsylvania. From 1875 to 1887 he was again in Italy, living for most of the time at Florence. He died at the State Mental Asylum at Middletown, New York.
Admiral Samuel Francis Du Pont (1884), Rockford Park, Wilmington, Delaware. Originally installed at DuPont Circle in Washington D.C.; moved to Wilmington, 1920.
Equestrian statue of General A. E. Burnside (1887), Burnside Park, Providence, Rhode Island. This was Thompson's only equestrian statue and last major work.
Medallion portrait of General John A. Dix.
Portrait bust of James Gordon Bennett.
Portrait bust of Samuel F. B. Morse, National Academy of Design, New York City.