The following year he was ordained to the priesthood at the Church of The Holy Communion, New York, on December 1, 1855, by Bishop Horatio Potter.

Brown was consecrated the first bishop of the Episcopal Diocese of Fond du Lac on December 15, 1875, at Cohoes, New York by Bishops Horatio Potter, Henry Augustus Bissell, William Croswell Doane, William Woodruff Mies, Benjamin Henry Paddock, Edward Randolph Welles, and John Scarborough.

According to a history of the diocese "The Council addresses of Bishop Brown, read in the light of later years, are wonderful examples of the conceptions he had of his high office.

"[2] During his episcopate, Brown established St. Paul's in Fond du Lac as his see city, set the groundwork for the establishment of a diocesan girls school, found a religious order, the Order of St. Moinica, shifting those congregations who still had pew rents to be "free churches", and worked to reach out to some disaffected groups of the Roman Catholic Church, especially in trying to work with René Villette.

Brown died of typhoid pneumonia in Fond du Lac on May 2, 1888,[1] and is buried in the churchyard of St. Paul's Cathedral.