Thomas Lee was born in Chestnut Hill, Massachusetts, the son of Colonel Francis L. Lee of Boston and Sarah (Wilson) Lee of Keene, New Hampshire. After graduating from Harvard College in 1879 and attending Harvard Law for a brief period, he worked in the Boston banking firm of Lee, Higginson and Company. After doing scientific work on expeditions to South America and Alaska with the United States Fish Commission and the Smithsonian Institute in Washington, he undertook the construction of the water supply system of Westport, New York and constructed the golf links there. He also designed the original Adirondack chair about 1900.
Thomas Lee never married, and was survived by his sister, Alice Lee of San Diego, California, by several nieces and nephews, the children of another sister, Mary (Lee) Hale of Albany, and those of his brother Francis W. Lee of Boston.