There are several studies looking into the differences between state-run and church-run schools in the recruitment and retention of their teachers. In Hungary, where teachers of church-run schools do not have to meet any special official requirements, church-run education has seen a rapid expansion since 2011. The denominational schools in Hungary are faith-based government-dependent private schools. The number of both Catholic and Protestant schools has increased twofold, and the expansion is still continuing. The vast majority of the newest denominational schools used to be run by the state and were taken over extremely rapidly, along with all their teachers and students, by the church. In our present study, based on our analysis of the survey “Teachers in church-run educational institutions” (2015–2017, N = 1134), we compare Catholic and Protestant teachers from church-run schools. Our results show that there are only slight differences in teachers’ values in the different denominational schools, which implies that the value systems of those schools are highly similar. The detected differences do not depend on the denominations that operate the schools but rather on the individual teachers’ religious affiliation. The most marked differences, however, have been detected between the value systems of religious and non-religious teachers.