Police said the students were charged with carrying out "subversive acts" after a "riot" in which they held lecturers and other students hostage at the University of Juba near Khartoum.
Riot police commander Major General Abdel Basit Saad Jubarah said 15 students were "slightly" injured in the unrest.
Police spokesman General Adel Sidahmed blamed the protest on southern students from the African National Front and supporters of the National Democratic Alliance.
The latter is an opposition unbrella group which includes the southern rebel Sudan People's Liberation Army.
The university includes northern as well as southern students and was originally based in the southern town of Juba, from where it was moved two decades ago when the SPLA launched Sudan's protracted civil war.
The SPLA is fighting the Khartoum government for a separate state in the south of the country.