The boy had been living in a juvenile shelter in Dachau before travelling to Turkey, reports Erasmus Monitoring, a blog which covers developments in the Islamist scene in Germany.
Newspaper Süddeutsche Zeitung confirmed the veracity of the story with security officials on Tuesday.
The blog reported that the boy, whom it identified as Erkan, travelled through Europe on a fake passport with a female cousin. Their goal was Raqqa, the "capital city" of Isis' self-proclaimed Islamic caliphate.
When his cousin was refused entry into Turkey, Erkan went on alone.
But, unable to speak Turkish or get in contact with an Isis member who was supposed to help him across the border, the teen logged onto Facebook to seek help.
It was at this point that the German Federal Office of Criminal Investigation (BKA) was able to catch up with him.
While the BKA had been trying to track Erkan down since he went missing the previous week, they had been unable identify his exact location.
But, by posing as jihadis on Facebook, they were able to get in contact with the youth via the site's chat function and persuaded him to give up his location under the pretense that they would help him across the border.
In cooperation with Turkish counterparts, they were then able to locate the boy and detain him.
The blog notes that a 15-year-old from Frankfurt successfully managed to cross the border on a previous occasion and died several weeks later in a battle with the Syrian army.
According to Ersamus Monitoring, Isis rarely has qualms about sending minors to their deaths.
The German Interior Ministry estimates that hundreds of Germans have crossed into Syria through Turkey to fight for the radical Islamist group.