Vlk was born in the hamlet of Líšnice, part of Sepekov parish, in the Písek District of Southern Bohemia. He spent his childhood in Záluží near Chyšky, where he attended elementary school and experienced the hard labour of farm work.
At the age of 11, he first started thinking about the priesthood. 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. The poster said: 'Wouldn't you like to become a priest?'. That goal seemed unattainable at the time, so he dreamed of becoming an aircraft pilot.
On 20 June1952 he passed his final examination at Secondary School in České Budějovice, Southern Bohemia. 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. He worked in various archives in Southern Bohemia: at the Regional Archives of Třeboň in Jindřichův Hradec, and from December 1960 to 1964 at the Civic and District Archives of České Budějovice, where he served as director.
In this same period he published a series of articles in various scientific reviews. In 1964 he left this work in order to study at the Theology Faculty of Saints Cyril and Methodius in Litoměřice (1964-1968).
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. From 1 November 1972 he was parish priest in Rožmitál pod Třemšínem and at the same time in Bohutín and Drahenice, in the Příbram district. There in 1978, the state authorities, in collaboration with the local communists, revoked his state authorization to exercise his priestly ministry.
Citizen Miloslav Vlk was thus forced to live underground in Prague from October 1978 to 31 December1988.
From 1978 to 1986 he worked as a window-cleaner in downtown Prague. In this period he secretly carried out his pastoral activity with small groups of lay people. From 1986 to 1988 he was able to work in the district archives of the Czechoslovak State Bank in Prague.
Between 1992 and 1993 he received three honorary degrees: one each from Illinois Benedictine College and the University of St. Thomas in the U.S., and a doctorate in theology from the Faculty of Passau. In addition to these academic awards he has also received various honorary citizenships.