He was born on 29 April 1928 in the town of Beveren-Leie (now a part of Waregem) in the province of West Flanders. He entered the Congregation of the Immaculate Heart of Mary (C.I.C.M. Missionaries) in 1946. He was ordained a priest in 1952. From 1953 to 1956 he studied canon law at the Catholic University of Leuven, Belgium and from 1962 to 1963 at The Catholic University of America in Washington DC. From 1955 to 1962 he was professor of canon law at the C.I.C.M. theological seminary in Leuven and from 1957 to 1962 assistant professor at the Higher Institute of Religious Sciences, Catholic University of Leuven, Belgium. He was vice-rector of the C.I.C.M. theological seminary in Leuven from 1956 to 1962. In 1963 he became rector of the Immaculate Heart mission seminary in Washington DC, where he served until 1966. In 1967 he came to Rome as General Secretary of the Congregation of the Immaculate Heart of Mary, a post he held until 1972.
Jan Schotte became a bishop in 1984 and an archbishop in 1985. On 26 November 1994 he was given the red hat of cardinal. Cardinal Schotte was the Secretary General of the Synod of Bishops from 1985 until 2004, leaving the post when Pope John Paul II accepted the resignation that Schotte had submitted in 2003 upon achieving the age limit. He was president of the Office of Labor of the Apostolic See from 1989 until his death.
Cardinal Schotte died on 10 January 2005 in the Agostino Gemelli University Polyclinic in Rome. He was buried in his Deaconry of Saint Julian of the Flemings in Rome. Had he survived Pope John Paul II, who delivered the homily at his funeral - the last while John Paul was alive -, Cardinal Schotte would, as the senior member of the order of Cardinal Deacons under the age of 80, have made the announcement of the next Pope's election.