John Wilton Nelson (born December 6, 1941, San Jose, Costa Rica, of American parents) is an American conductor. Nelson studied at Wheaton College, and later at the Juilliard School of Music with Jean Morel .

Nelson was Music Director of the Indianapolis Symphony Orchestra from 1976 to 1987. Nelson made two commercial recordings with the Indianapolis Symphony, of music by Ellen Taaffe Zwilich and Charles Martin Loeffler, for the New World Records label. 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 September 1998, Nelson became Music Director of the Ensemble Orchestral de Paris. In March 2007, it was announced that he would leave this position with the Ensemble Orchestral de Paris at the end of the 2007-2008 season.