The youngster, thought to have been radicalised only recently, was detained in a special forces operation late Tuesday at a shelter for asylum seekers in the western city of Cologne, police and local prosecutors said in a statement.
Information gathered from the teenager's mobile phone indicate he was in touch with a person abroad who had ties to Isis and "wanted to recruit the young Syrian for Islamist activities", the statement said.
Germany's state security authorities believe the youngster posed a "serious threat" and have assigned a 35-strong team of investigators to the case.
Germany is on edge after suffering two attacks claimed by Isis in July - an axe rampage on a train in Würzburg and a suicide bombing in Ansbach. Both were carried out by asylum seekers.
In Würzburg, the 17-year-old attacker was shot dead by police after injuring five people.
In Ansbach, 15 people were injured after a Syrian failed asylum seeker detonated an explosive device outside a music festival, killing himself.
The attacks rattled Germans' sense of security and fuelled concerns over the country's record influx of migrants and refugees last year.