Now aged 15, the boy who comes from a Turkish background, is accused of “participating in a terrorist group”. His case will be heard at a Sankt Pölten court, west of the capital.
Arrested at school in October 2014, police said the boy has admitted he was trying to make a bomb, and that he was planning to plant it at one of Vienna's main stations.
Investigators said they found Isis propaganda images on his computer, phone and video game console.
Prosecutors said he was “actively” seeking to make a bomb, but his lawyer Rudolf Mayer told AFP he had only been “playing with the idea”.
The teenager has also admitted he wanted to travel to Syria to join Isis's ranks. He broke his bail conditions and tried to flee in January with a 12-year-old friend, with both apparently trying to reach the war-torn country.
Because of his age, the maximum sentence he could face is five years in prison.
According to unconfirmed press reports, Isis had promised the teenager €25,000 ($28,000) to commit the Vienna attack.
Officials in Vienna say at least 200 people from Austria, including women and children, have travelled to Syria and Iraq, where Isis controls vast swathes of territory and commits horrific abuses.
Some 70 suspects have since returned to the country, and several of them are in custody pending judgement.