The formal indictment of 18 politicians and activists issued Friday by Spain's public prosecutor's office accuses Junqueras of being the main promoter of an illegal Catalan independence referendum.
The banned vote in the northeastern Catalonia region caused Spain's gravest political crisis in four decades of democracy.
A Spanish Supreme Court probe into the turbulent events was wrapped up last month and the trial is expected to begin in early 2019.
Seven politicians, including Junqueras, and two civil society activists are already in pre-trial custody in Catalan prisons.