Charles Henry Sanborn was born in Hampton Falls, New Hampshire, to Aaron and Lydia (née Leavitt) Sanborn. Charles Sanborn's brother, Franklin Benjamin, was a well-known writer and social activist closely aligned with the circle of American Transcendentalists including Henry David Thoreau and Ralph Waldo Emerson. Charles Sanborn received his M.D. from Harvard University in 1856. He spent his career practicing medicine in his hometown, where he also served as a Justice of the Peace, deputy secretary of state in 1846, and representative in 1854 and 1855. He married Elizabeth Brown, with whom he had one daughter, Annie L.