Scola in 1995 resigned as bishop of Grosseto to serve as rector of the Pontifical Lateran University in Rome and President of the Pontifical John Paul II Institute for Studies on Marriage and Family in Rome, with a term spent as visiting professor at the counterpart Institute in Washington, D.C., during which time he wrote a monograph on the theology of von Balthasar.
In 1995 he became a member of the Congregation for the Clergy. He also served as member of the Episcopal Commission for Catholic Education of the Italian Bishops' Conference and, from 1996, as president of the Committee for Institutes of Religious Studies which addresses questions of the theological formation of the laity in Italy.