Following the death of Cassidy, Connolly became Bishop of Fall River in May 1951. One key to his tenure as Bishop was a special concern with providing secondary education in the four urban areas of the Diocese. As a result, four Catholic high schools were constructed under his guidance. Bishop Connolly High School was dedicated in his name in 1967. He also founded the diocesan newspaper, "The Anchor". Connolly attended all four sessions of the Second Vatican Council. He served as Bishop of Fall River until 1970 when he retired.