The department was abolished in 1970 and Vopěnka, though allowed to stay at the university, fell into disfavour with the regime, which limited his contacts with foreign mathematicians.

During the period June 1990 – July 1992 he served as Minister of Education of the Czech Republic (then part of Czechoslovakia).

In this position he, without much of success and facing protests from the teachers, attempted to institute school reforms.

Until 2009 Vopěnka worked as a professor at the Jan Evangelista Purkyně University in Ústí nad Labem, in the Department of Mathematics of the Faculty of Science.

Petr Vopěnka also participated in translation and publishing of early mathematical texts (such as works of Euclid and Al-Khwarezmi) into the Czech language, and then he worked at the Department of Philosophy and Department of Interdisciplinary Activities, University of West Bohemia in Plzeň.