He is an alumnus of Michigan State University. While attending Michigan State University he joined the Delta Upsilon Fraternity. As Paul in the Peter, Paul and Mary trio, he participated in one of the best known mass-media ensembles of the 1960s phase of the American folk music revival, and included some of his solo songs and extended monologues in their performances and recordings.
His best-known composition is "The Wedding Song (There is Love)", which charted in 1971 and remains popular for performance during wedding services. He wrote the song as a wedding gift for Peter Yarrow, and refused to perform it for the public until Yarrow requested it at a concert where his wife was present. Stookey assigned the copyright to this song to the Public Domain Foundation.
In addition to his recordings with the trio, he released a number of solo works, several albums with an ensemble called Bodyworks, and some anthologies. His post-Peter, Paul and Mary works have emphasized his Christian faith, family life, and social concerns. He was an important artist in the young Jesus music movement which would later bloom into the contemporary Christian music industry, although his generally liberal political views distinguish him from many such artists.
He remains active in the music industry, performing regularly both as a member of Peter, Paul, and Mary and as a solo act.
Though Stookey spent several years as a school-year resident of Massachusetts while his wife Betty served as the Northfield Mount Hermon School chaplain, Noel and Betty returned to their home in Blue Hill, Maine in June 2005, where he records in a studio that was previously a chicken-house.