On October 4^th, 1988, Pope John Paul II along with Archbishop Achille Silvestrini and Bishop Juozas Preikšas consecrated Juozas Bačkis as bishop. The Archbishop of Vilnius Julijonas Steponavičius came to Rome for the first time for the celebration. In the same year, he was appointed as a titular Archbishop of Meta and as a Nuncio in Holland.

On December 24^th, 1991 Pope John Paul II created a Church Province for Vilnius, and appointed Audrys Juozas Bačkis as Archbishop Metropolitan of Vilnius. He was ordained on March 3^rd, 1992. From 1992–1993, he was in charge of Pope John Paul II Apostolic Journey to Lithuania (September 4^th-8^th, 1993). He chaired the Lithuanian Bishop’s Conference from 1993–1999 and again from 2002–2005. In 1999, he was assigned by Pope John Paul II to be Vice President of the European Bishop’s Synod Member Committee and the final closing presentation. From 1998–2001 he was in charge of the Lithuanian Bishop’s Conference Anniversary Committee.

On February 21^st, 2001 he was appointed as Cardinal by the Holy Roman Catholic Church. Since 2001, he is a member of the Catholic Upbringing Congregation. From 2001–2007, he was a member of the Pontifical Church Cultural Heritage Commission. From 1992–2011 he was a member of the Pontifical Societal Communication Committee.

In 1993, he re-established the Vilnius Seminary. In the same year, due to his initiative, a Theology Department was established at the Vilnius Pedagogical Institute, where Religion teachers were trained. He has been a patron of the Faith and Light Community, which helps unite families who are raising disabled children. He has done so since he first arrived in Vilnius. He helped to build Versmė School, which provides integrated Catholic-oriented education where children with disabilities study together with healthy children. He is the Spiritual Father of this school. In 1992, he established the Betanija Food Shelter which feeds about 500 people cost-free every day. Approximately 100 children from large or troubled families are fed at the Caritas cafeteria also run by the Archdiocese. In 1996, the Mother-Child Home was established. Young, marginalized, homeless, unmarried women live there. In 1999, the Mother of Mercy shelter was opened. Mother Teresa’s sisters feed approximately 150 people there, and treat sick, homeless people. In the same building, there are about 50 homeless people that take warm shelter there for the night. Caritas continues to expand their organization’s activities through parishes, they collect donations for the homeless and encourage sharing bread and love. Caritas staff often visits hospitals, prisons and nursing homes. In 1994, the Family Center was established. Couples attend Pre-Cana classes there. They receive spiritual and psychological consultation.

In 1997, the Trinapolis Retreat House was created where there are regular retreats for children, adolescents, group, clergy, and even for individuals. In 1999, the Vilnius Archdiocese Pastoral Care Center was opened, where various Catholic organizations meet. In 2001, a Trade-Craft Center was opened where professional craftsmen help young individuals learn the crafts of carpentry, jewelry-making, building and restoring, cook, tailor or seamstress. In 2001, in memory of his father, Dr. Stasys Bačkis, a chapel was built at Vilnius University’s Santariškių Clinics with funds from his late father’s estate and other donations.

On April 30^th,1997, Vilnius Pedagogical University granted Archbishop Bačkis an honorary Doctorate. On February 16^th, 2000, he received a Second Degree Order of Grand Duke Gediminas. On February 16^th, 2003, he was presented with the Vytautas Didysis Order’s Great Cross. On May 13^th, 2003, he received an Honorary Doctorate from Krakow’s Pontifical Theological Academy.

On April 5^th, 2013, he resigned according to the rule of Canon Law, which was approved by Pope Francis. He continued his obligations until the ordination of Gintaras Grušas as Archbishop of Vilnius on April 23^rd.