On December 30, 1964, Freking was appointed the sixth Bishop of La Crosse, Wisconsin, by Pope Paul VI. He was installed on February 24, 1965. From 1964 to 1966, he headed the National Catholic Rural Life Conference. During his tenure in La Crosse, he reduced the diocese's debt from $11 million to $4 million between 1965 and 1981. He established a diocesan commission on Christian renewal in 1965, and the first lay ministry training program in the United States in 1975.