The teenager, who is from a Turkish family, was detained for a second time in January on suspicion of terrorism-related activity.
He was released from custody in November last year but then ran away and failed to abide by his probation agreement.
Police found him in a fast food restaurant in Vienna after his mother reported him missing.
He was allegedly planning to travel to Syria and had been plotting a series of bomb attacks at crowded targets such as Vienna’s Westbahnhof railway station. The Islamic State is reported to have offered him money to carry out such a terror attack.
The authorities have based their charges on data found on the boy’s PlayStation games console, including bomb-building plans downloaded from the internet, Michaela Obenaus, a spokeswoman for prosecutors in St Pölten said.
The teenager faces up to five years in jail if convicted of supporting a terrorist organisation and planning an attack.
More than 170 people have left Austria to fight in the Middle East, according to the interior ministry, some of whom have been killed.