Ramon Rigal from the Church of God in Cuba was charged earlier this year after deciding to home school his children.
He and his wife made the decision because they felt that state school teaching emphasised a Marxist-Leninist atheist ideology which conflicted with their Christian faith.
He was sentenced to one year in a prison but that was later reduced to one year's house arrest.
Pastor Rigal has since been told he can no longer work as a pastor.
Religious freedom charity Christian Solidarity Worldwide (CSW) believes this is part of a wider crackdown on the faith.
The charity says several cases have been brought to light in recent months in which family members of church leaders and activists are singled out for harassment and discrimination by the authorities.
CSW's Senior Advocacy Officer for the Americas, Anna Lee Stangl, said: "The punishment meted out to Pastor Ramon Rigal and his wife is unwarranted and places the family in undue hardship. We call on the Cuban authorities to repeal the sentences against the pastor and his wife, and to allow him to continue his work as a church leader."