In 1994 he returned to Rome, where he worked in the Slovak Radio and the Vatican department in addition, he studied spirituality from which in 1996 at the Pontifical Oriental Institute, defended his doctoral thesis on "P. Michal Lacko - teacher formatter and Greek Catholics."

He replaced On 11 December 2002, Pope John Paul II named him the 10th Eparchal Bishop of Prešov, being consecrated in St. Peter's Basilica in Vatican City on 6 January 2003 by the Polish Pontiff.

On 30 January 2008, Babjak was appointed by Pope Benedict XVI as the first Metropolitan of Prešov and also promoted to the rank of Archeparch.

The enthronement of the first Archeparch and Metropolite Ján Babjak took place on Sunday of 17 February 2008 in Prešov Cathedral of St. John the Baptist in Prešov and the celebration elevation of Greek Catholic Church in Slovakia to the level of sui iuris church occurred in the city hall.

On 25 April 2022, Pope Francis accepted Ján Babjak's resignation prior to reaching the canonical age and named Peter Rusnák Greek Catholic Eparchal Bishop of Bratislava the apostolic administrator to the vacated Archeparchy of Prešov.