Petra and Dirk Wunderlich were educating their four children at home in August 2013 when police carried out a raid and removed the children.
They were later returned.
After courts in Germany ruled in favour of the government, the European Court of Human Rights agreed to take up the case in August 2016.
Now that court has backed the German government.
In today's (Thursday's) ruling in Strasbourg in the case of Wunderlich vs Germany, the ruling stated that the German authorities' actions were not in violation of the Wunderlich family's fundamental rights.
Robert Clarke is from ADF International which was supporting the family.
He told Premier he was disappointed by the ruling:
"This is a ban that Germany enforces with criminal penalties. It's a ban that they enforced in this case by sending more than thirty police officers and social workers to surround the home of the Wunderlich family to threaten to use a battering ram to open the door and then to carry out four children crying."
In a statement, he said:
"We are extremely disappointed with this ruling of the Court. It disregards the rights of parents all over Europe to raise their children without disproportionate interference from the state. Petra and Dirk Wunderlich simply wanted to educate their children in line with their convictions and decided their home environment would be the best place for this. Children deserve this loving care from their parents. We are now advising the Wunderlichs of their options, including taking the case to the Grand Chamber of the European Court of Human Rights,"
Germany is one of a minority of countries in Europe that do not allow home schooling for children.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.