Huntington was born in Lowell, Mass. He graduated at Harvard in 1859 and in 1859–1860 was an instructor in chemistry there. Entering the Episcopal ministry, he was rector of All Saints Church, Worcester, Massachusetts, in 1862–1883 and of Grace Church, New York from 1883 until his death. Dr. Huntington always took a prominent part in public affairs. He was active in the movement for liturgical revisions and was long chairman of the Prayer-Book Revisions Committee, and editor with Dr. Samuel Hart of the Standard Prayer-Book of 1892.