The man named only as Fabian G., 26, is being held in in Kurdish custody in northern Syria, according to his German lawyers Seda Basay-Yildiz and Ali Aydin.
He went to Syria in 2014 with his brother to join ISIS terrorists.
He claims officials told him he would be able to leave the country if Germany made an official application for his deportation – but one has not been submitted.
His lawyers said: “From our point of view the German federal government is constitutionally obliged to return Fabian G. back to Germany. To date the Federal Republic of Germany has not done so.
“Political motives are the reason behind their failure to do so.”
They added: “This is due to their responsibility to protect and trust.”
Miss Basay-Yildiz said she has been racially abused and her family has been threatened after representing alleged ISIS fighters in other cases.
The lawsuit has been filed with the administrative court in Berlin but a trial date is yet to be set.
The German foreign ministry confirmed that it does not have any diplomatic relations with the Syrian government.
In a statement it said: “The German government cannot guarantee legal and consular duties for jailed German citizens due to the armed conflict there.”
There is no mention on the whereabouts of Mr G’s brother.
Their father has been fighting his son’s return.
He alleges he was notified that his sons had been killed in battle in 2016 by the State Protection Office in Kassel, a city in central Germany.
But he said he was sceptical they were killed and was convinced they were still alive.
In Spring 2019, he travelled to northern Syria and says he was able to identify one of his sons from a distance in a prison.