Born on April 12, 1830, in Boston, Massachusetts, he became an ardent supporter of the Oxford Movement, an affiliation of High Church Anglicans that led to Anglo-Catholicism in The Episcopal Church.
A graduate of Phillips Academy, Andover in 1846, in 1853 Grafton graduated from Harvard University with a degree in law, but he found himself drawn toward the ordained ministry. Grafton studied theology under William Whittingham, Bishop of Maryland, and was ordained deacon on Dec. 23, 1855.
Grafton began his ordained ministry as assistant at Reisterstown, Maryland. On May 30, 1858, he was ordained priest. He then served as curate at St. Paul's Episcopal Church in Baltimore and chaplain of the deaconesses of the Episcopal Diocese of Maryland.
At the close of the Civil War, Grafton went to Britain. With Richard Meux Benson and Simeon Wilberforce O'Neill he co-founded the Society of St. John the Evangelist (SSJE), also known as the Cowley Fathers.
Grafton returned to the United States and, in 1872, became fourth rector of the Church of the Advent in Boston. A jurisdictional dispute concerning Grafton's overseas religious superior led to his withdrawal from the SSJE. Grafton also helped establish the American Congregation of Saint Benedict (now known as the Benedictine Order of St. John the Beloved); and in 1888 he was a founder of the Sisterhood of the Holy Nativity, along with Mother Ruth Margaret.
Grafton was consecrated bishop on December 15, 1888 at the Cathedral Church of St. Paul the Apostle, Fond du Lac, Wisconsin by William E. McLaren, Bishop of Chicago; Alexander Burgess, Bishop of Quincy; and George F. Seymour, Bishop of Springfield. During his tenure as bishop, Grafton spearheaded a great expansion the Episcopal Diocese of Fond du Lac, much of it driven by contributing much of his own personal wealth and soliciting contributions from many of his wealthy friends back east. He also left behind a legacy of printed works, sermons and essays.
In 1900 Grafton was chief consecrator of Reginald Heber Weller as bishop coadjutor of Fond Du Lac. The liturgy of the consecration was controversial. The Russian Orthodox bishop of Alaska, Saint Tikhon was present as well as Antoni Kozlowski of the Polish National Catholic Church. Grafton was photographed with these other bishops wearing copes and miters (which was not widely accepted in the Episcopal Church at that time). The photo became known as the "Fond du Lac Circus".
Grafton is honored with a feast day on the liturgical calendar of the Episcopal Church (USA) on August 30.