Police fired tear gas and wielded batons while the university students fired back with stones, an AFP reporter witnessed Emergency vehicles wailed across the city as the protest continued into the early afternoon.
The students' exact demands were not immediately clear but their action coincided with the first day of exams, which they boycotted with a sit-in at the University of Khartoum campus along the Blue Nile river.
A crowd of students estimated in the hundreds flowed into surrounding streets, where the confrontation with police occurred, the reporter said. It was not known whether anybody was detained.
Riot police in Khartoum used tear gas and beat demonstrators last week at two other protests, held in support of residents displaced by the giant Merowe dam.