They accuse the man, a German citizen named as Kerim Marc B., of having taken part in weapons training and fighting in battles on the side of Isis in Syria.
The man left Germany in March 2013 and travelled to Syria via Turkey, where investigators say he had joined up with Isis by October.
After a brief trip back to Germany in early 2014, he returned to the warzone in Syria in July and took up arms again.
Prosecutors in Düsseldorf said they were originally investigating Karim Marc B. for planning a serious crime against the state in Germany, and only later became aware that he had in fact joined Isis.
He will be brought before a judge on Thursday to decide on the terms of his custody while the investigation continues.