This initial idea of a priestly vocation came to him because he felt particularly challenged by a poster hanging in his parish church that continued to attract his attention.

In those years of Communist persecution theological studies were impossible, so from 1952 to 1953 he worked at the Motor Union automobile factory in České Budějovice and from 1953 to 1955 did military service in Karlovy Vary.

Despite the political situation, after being discharged he was able to study archival science at the Arts Faculty of the Charles University in Prague and received his degree in 1960.

On 23 June 1968, during the 'Prague Spring', he was ordained a priest at the age of 36 and was immediately appointed secretary to Bishop Josef Hlouch of České Budějovice (1968–1971).

The state authorities, worried about his influence and pastoral activity, forced him in 1971 to leave České Budějovice and sent him to the parishes of Lažiště and Záblatí, isolated on the mountains of the Bohemian Forest in the Prachatice district.

Subsequently, on 1 September 1989, he began to work as a curate on the Bavarian (German) border: at Čachrov, Javorná, Železná Ruda, Běšiny and Stráž na Šumavě.

On 27 March 1991 Pope John Paul II appointed Vlk Archbishop of Prague to succeed Cardinal František Tomášek.

He was a member of the following dicasteries of the Roman Curia: Pope Benedict XVI accepted Cardinal Vlk's resignation as Archbishop of Prague on 13 February 2010 and nominated Dominik Duka to succeed him.

Local organizers responded that Vlk showed "ill will to socially ostracize Catholics who point to the negative consequences of liberalization processes in the church.