The 58-year-old Archbishop of Olomouc was elected at a plenary meeting in Prague on Wednesday, according to the Bishops' Conference.
Nuzik succeeds Archbishop Jan Graubner (76) of Prague, who has held the presidency since 2020 and before that from 2000 to 2010.
Pope Francis appointed Nuzik as Archbishop of his home diocese of Olomouc in February 2024.
He was previously an auxiliary bishop there and has been the interim head as diocesan administrator since 2022.
Located in the east of the country, the archdiocese is considered a Catholic stronghold in the otherwise rather secular Czech Republic.
It is the only church area in the country where Catholics make up more than half of the population.
The Bishops' Conference elected its previous Secretary General, the Bishop of Leitmeritz in North Bohemia, Stanislav Pribyl (53), as Deputy Chairman.
At the last census in 2021, 741,000 people in the Czech Republic professed allegiance to the Catholic Church.
This makes it the largest religious community in the country with a population of ten million.