From 1968 to 1970 he was a prefect at a Catholic seminary in Bratislava, before working again as a chaplain in Sereď in 1970–71, and was a dean there until 1975.

On 14 February 2008, Pope Benedict XVI appointed him as the Archbishop of the newly reformed Archdiocese of Trnava, which remained an Archdiocesis despite no longer being metropolitan.

[1] In accordance with the canon law, upon reaching 75 years of age, he requested to be released from his office.

Pope Benedict XVI named Róbert Bezák as his successor on 18 April 2009.

Ján Sokol is listed as having cooperated with the former Communist Czechoslovak secret police, according to the documents from Ústav pamäti národa (ÚPN, Nation's Memory Institute), however, he denied any cooperation.