John Wilton Nelson (born December 6, 1941, San José, Costa Rica, of American parents) is an American conductor. His parents were Protestant missionaries.

Nelson studied at Wheaton College and later at the Juilliard School of Music with Jean Morel. Nelson was music director of the Greenwich Philharmonia in Connecticut and the New Jersey Pro Arte Chorale, and also served on the conducting staff of the Metropolitan Opera. In 1972, he conducted his New York City opera debut at Carnegie Hall in an uncut performance of Berlioz's Les Troyens. With the Metropolitan Opera, his professional opera conducting debut was also with Les Troyens, on one day's notice as an emergency substitute for Rafael Kubelík.

Nelson was music director of the Indianapolis Symphony Orchestra from 1976 to 1987, making commercial recordings there of music by Ellen Taaffe Zwilich and Charles Martin Loeffler for New World Records. With Opera Theatre of Saint Louis, he was music director from 1985 to 1988, and principal conductor from 1988 to 1991. He was also music director of the Caramoor Festival in Katonah, New York, from 1983 to 1990. In 1998, Nelson became music director of the Ensemble Orchestral de Paris (now renamed the Orchestre de chambre de Paris), a position he retained for ten years.

Nelson's interest in choral music led to his position as artistic director of Soli Deo Gloria.

Nelson and his wife Anita had two daughters. Anita Nelson died in October 2012. Nelson now lives in Chicago with his daughter, as well as in Costa Rica.