A Brooklyn federal grand jury returned the superseding indictment, charging James with 10 counts of committing a terrorist attack or other violence against a mass transportation system and vehicle carrying passengers and employees.
James is also facing one count of discharging a firearm during a crime of violence.
James had previously pled not guilty to a single terrorism offense.
James' attorneys previously said his rights were violated by the FBI after his arrest. They argued that FBI agents took oral DNA samples from Frank James without informing his legal team.
They also say he was improperly questioned in his jail cell and claim agents had him sign several documents.