Huntington was born in Oneonta, New York. After working in the hardware business and owning a sawmill, he went to work with his uncle Collis Huntington on the Southern Pacific Railroad. When Collis died in 1900, Henry inherited much of his uncle's fortune, which he sold and used to establish the Pacific Electric Railway.
In 1903, Huntington began collecting rare books and manuscripts; this was the beginning of Huntington Library, which also included an art collection and botanical gardens on his estate in San Marino, California.
After Huntington died in Philadelphia, his library, art collection, and botanical gardens were opened to the public.