Pope John Paul II appointed him the Archbishop of Zagreb on July 5, 1997. Bozanić took over his service of Archbishop of Zagreb and Metropolitan on October 4 of the same year in the Zagreb Cathedral from his predecessor Cardinal Franjo Kuharić.
He was elected president of the Croatian Bishops’ Conference that year as well, office he held for two consecutive terms till 2007. As the Archbishop of Zagreb he is the Great Chancellor of the Catholic Faculty of Theology of the University of Zagreb and Great Chancellor of the Catholic University of Croatia.
At the 36th plenary session of the Croatian Bishops’ Conference in 2008 he was elected president of the CBC's Commission for relations with the European Union and at the 41st plenary session of the CBC in 2010 the vice president of the CBC and president of the episcopal commission of the CBC for state relations.
In April 2001 he was elected first vice president of the Council of European Bishops' Conferences (CCEE) and in 2006 he was re-elected to the same duty for another term. He participated in the first ( in 1991) and the second (in 1999) Special Assembly for Europe of the Synod of Bishops. At the second one, he was elected member of the Special Council of the General Secretariat for Europe of the Synod of Bishops in Rome on the topic: The Word of God in Life and Mission of the Church.
He is a member of the Congregation for Divine Worship and Discipline of Sacraments, Congregation for Catholic Education, Pontifical Council for the Laity and newly established Pontifical Council for Promoting New Evangelization as well as a member of several special commissions of the Holy See.
In 1998, as the Archbishop of Zagreb and president of the CBC, he greeted Pope John Paul II in Zagreb during his second official papal visit to Croatia and in Marija Bistrica at the ceremony of beatification he asked him to beatify Cardinal Alojzije (Aloysius) Stepinac. In 2003, once more as the president of the CBC, he greeted Pope John Paul II during his third official papal visit to Croatia when he visited Rijeka and Trsat, Dubrovnik,Osijek, Đakovo and Zadar.
On October 21, 2003 Pope John Paul II elevated him to the College of Cardinals of the Roman Catholic Church at the ceremonious Consistory in Rome.
He participated in many international symposiums in Croatia and abroad and published several scientific articles in Croatian and international publications. In 2008 his books: Istina u ljubavi i Blaženi Alojzije Stepinac – baština koja obvezuje [Truth in love and the Blessed Aloysious Stepinac – a binding heritage – tr.] were published, and in 2009 one more was published: Čovjek, Crkva i domovina u otajstvu Uskrsa i Božića [Man, Church and Homeland in Mystery of Easter and Christmas - tr].
His latest book: Krist vas zove. Poruke mladima [Christ is calling you. Messages to youth] was published in 2011 and is dedicated to youth who have shown their enthusiasm in their meeting during the official papal visit of Pope Benedict XVI to Croatia.
Pope Benedict XVI appointed him member of the Pontifical Council for Social Communications on December 29, 2011.