On Tuesday, authorities said a group of teens on the trail approached the jogger and one them hit the man in the back of the head.
A few hours later, police caught up with the 13-year-old believed to be responsible and took him into custody.
It is the fifth reported attack in just three months.
Durham police said they've increased patrols on the trail since May after reports of other assaults, including a man who attacked a female runner just last month.
The most recent incident has renewed some fears and concerns, with some citizens calling for plain-clothed officers to patrol the trail.
"I've seen police, sometimes on bikes or motorcycles," Durham resident William Jackson said. "I just try to be precautious, mindful of my surroundings. They said not to ride around dusk."
Vigilance alone, some said, isn't the cure-all. The attacks have happened even during the day.
Letters to Durham's mayor and other city leaders have already poured in. One person wrote that his friends and family have sadly curtailed their use of the trail.
The most outraged letters came from assault victims, who demanded action telling them to "take back the trail."
Another victim, who was mugged last year, wrote that these are not isolated cases and doing nothing would "put lives at risk."
Durham police say they have both uniformed and undercover officers on the trail, but when asked how many and when they won't say.
Durham Mayor Bill Bell insisted that the trail is safe. He told ABC11 that security changes are now in the works. Exactly what they are is unclear.
"We're going to enhance things by that I don't want to give anything away in terms of what the police are doing," said Bell. "I guess for those people who might be thinking about doing something. They should know they'll be out there and it's not going to be easy to do something as they think it is."
Police are also asking visitors to avoid groups of people lingering on the trail.