The 18-year-old was arrested on Monday morning at Frankfurt airport, said the state prosecutor.
The man is alleged to have left Germany by car In October with two male companions and a 19-year-old woman, reaching Syria via Turkey, where they wanted to take part in the conflict between Isis and the Syrian government.
“We are assuming that he fought there,” Chief prosecutor Doris Möller Scheu said.
At the end of February the man, who was born in north Hesse, is alleged to have attempted to return from Syria to Turkey. He was arrested at the border and transported back to Germany.
The suspect has not responded to the accusations. It is unclear whether his companions are still in Syria.
At the beginning of March a suspected Isis member was arrested at Düsseldorf airport. The federal court had issued an arrest warrant for the 22-year -old.
According to a recent statement by the Interior Minister, Thomas de Maizière, some 650 Germans have travelled to the war zones in Syria and Iraq.
De Maizière also said that there were about 1,000 high risk individuals in Germany who the security services are keeping an eye on.