After three years, he was sent to the Pontifical Ecclesiastical Academy in Rome to finish his studies in canon law. After earning a doctorate in 1966, he entered the diplomatic service of the Holy See, serving in nunciatures in Cuba and Egypt. He was called to Rome in 1975 to work in the Secretariat of State until he was appointed Permanent Observer at the Council of Europe in Strasbourg in 1979.
On 12 February 1983 he was appointed titular Archbishop of Mevania and was ordained in the Basilica of Saint Francis of Assisi on 23 April 1983. He also served as Apostolic Delegate to Angola (February 1983) and as Pro-Apostolic Nuncio in São Tomé and Principe (May 1985).
Thereafter, he became Apostolic Nuncio in the Dominican Republic (20 April 1991), Peru (23 April 1994) and in France (19 June 1999).
On 2 June 2009, Pope Benedict XVI appointed him Major Penitentiary.
Major Penitentiary emeritus, 5 January 2012.
Created and proclaimed Cardinal by Benedict XVI in the consistory of 20 November 2010, of the Deaconry of San Anselmo all’Aventino (Saint Anselm on Aventino).
Cardinal Fortunato Baldelli died on 20 September 2012.