The youth shouted slogans and pelted stones at the forces near the venue in Hazratbal area of the city, police said.
The security personnel fired teargas shells to disperse the protesters at Habak Crossing. "The situation is under control now," police said.
The were no reports of any injuries.
The 21-km half marathon was flagged off in the morning from the Kashmir University at Hazratbal. It was to pass through the banks of Dal Lake along Foreshore Road.
As many as 15 international athletes had confirmed their participation in the event for which more than 15,000 people had registered.