Merkan G., who is of Turkish origin and from Lower Austria, was found together with a schoolfriend - a 12-year-old boy from Afghanistan who was reported missing on Wednesday.
Merkan G. is now in police custody but police said they have no reason to detain the 12-year-old, who will be returned to his parents. There is no evidence that the younger boy had any connection with terrorist activities.
The boys were arrested at around 7am in a fast food restaurant in Vienna’s Mariahilf shopping district by a Vienna police unit.
"The 14-year-old will be transferred during the day to St. Pölten prison," police spokesman Markus Haindl said.
Merkan G. went missing on Tuesday, before he was due to start a period of probation in a remand home in Hütteldorf, Vienna. Police focussed their search for him on Vienna, and raided mosques on Friday morning.
The teenager was first arrested in October and authorities have said they believe the boy was planning to travel to Syria to join the Isis terror group, and had researched how to make a bomb, with Vienna's crowded Westbahnhof railway station one of several potential targets.
In Austria, young people are considered criminally culpable from the age of 14.