On March 9, 2004, Pope John Paul II appointed Cunningham as the 13th Bishop of Ogdensburg. Cunningham was ordained and installed as the bishop of Ogdensburg on May 18, 2004 at St. Mary's Cathedral in Ogdensburg. The diocese has more than 128,000 Catholics in the eight northernmost counties of New York state covering an area of 12,036 square miles.
In the United States Conference of Catholic Bishops, Cunningham has served as chairman of Region II (Province of New York). He currently serves as a representative from Region II to the Administrative Committee of the United States Conference of Catholic Bishops. He also serves on the Committee for Priorities and Plans, as well as on the Committee for the Protection of Children and Young People and the Sub-committee on Native American Catholics.
"Sent by Pope Benedict XVI, I come to teach and preach the word of God; to love you with wholehearted affection and to serve your needs especially as a minister of the Eucharist and reconciliation. I hope to be a source of unity for the diocese," Bishop-designate Cunningham said.
As bishop of Syracuse, Cunningham will be the shepherd of more than 250,000 Catholics who reside in seven counties of the diocese covering 5,479 square miles.