Zschäpe was being charged as an accessory to the murder of 10 people, Germany's Attorney General Harald Range announced on Thursday.
Four people suspected of helping the NSU group will face the same charge, though not in all ten cases.
They were named as Carsten S., Andre E., who is thought to have helped the NSU carry out a nail-bomb attack in Cologne, Holger G., who faces three charges of accessory to murder, and former National Democratic Party functionary Ralf Wohlleben.
The higher regional court in Munich is to handle the trial, and the defence teams of all the suspects are to receive the formal charges in the next few days. They amount to around 500 pages, Die Welt newspaper reported. The trial is not expected to start until next spring.
German Interior Minister Hans-Peter Friedrich welcomed the announcement, saying, "The charges have been made, and I think we can see from that the investigation is moving forward."
Up to 400 officers are thought to have worked on the year-long investigation which followed the dramatic events of November 4, 2011, when the existence of the NSU first came to light.
That was when two of the group's three members - Uwe Mundlos and Uwe Böhnhardt - were cornered by police after a botched bank raid. Surrounded by police, Mundlos shot Böhnhardt and then himself in a caravan. Zschäpe approached the police voluntarily a few days later, but not before she allegedly destroyed evidence by setting fire to the trio's shared flat in Zwickau, Saxony.
Before then, the NSU spent a decade carrying out killings, bombings and bank robberies - between 2000 and 2007, they are thought to have murdered nine small-business owners of immigrant background and a German policewoman.
Over the past year, a parliamentary committee has uncovered systemic failure in the German security forces' attempts to track down the NSU, despite having several informants within the neo-Nazi scene who were close to the trio. Several high-profile intelligence chiefs have resigned amid reports of file shredding and obstruction.
Friedrich recently defended the security forces against accusations that they had been obstructing the committee's investigation, and said the "internal operations" of the secret service had to be protected.