Eric Andrews, 40, turned himself in to police after the incident.
According to the Highway Patrol, 38-year-old Trooper Anthony Scott was at the residence at the time, but officials haven't said why.
The Highway Patrol would only say that the trooper who was at the woman's house was on duty, but had not been dispatched to the location and was not there for official business.
A spokesperson says if a trooper is caught having an extra marital affair there would be consequences.
"If it is substantiated that it is sex on duty then I can tell you the trooper will lose their job over that if it's proven to be true." N.C. Highway Patrol Capt. Everett Clendenin said.
Andrews has been charged with felonious assault by strangulation, felonious second degree kidnapping, assault by pointing a gun, assault on a female, and communicating threats.
He was jailed under a $1,000,000 secured bond and scheduled to appear in Chatham County District Court in Pittsboro on September 14.