The incident happened around 10:13 p.m. along Route 144, in the area of the Monocacy River.
Dfc. Greg Morton observed a vehicle driving erratically along the route, and pulled the car over. Officials say the Morton placed the female driver in custody for an emergency evaluation.
As Morton was securing the woman in the rear of his cruiser to take to Frederick Memorial Hospital, a passing vehicle's mirror struck him.
Dfc. Morton was taken to R Adams Cowley Shock trauma Center in Baltimore Wednesday night by a Maryland State Police helicopter.
Sheriff Chuck Jenkins is reminding the public to be remember the Move Over Law.
"He's home recovering. We're thankful the injuries weren't extremely serious. It's always a risk when deputies are out making stops on the road," said Frederick County Sheriff Chuck Jenkins. "The new laws were passed, the Move Over Laws, which force vehicles to move over to the left lane, if there is a left lane, if not they're to slow down when they pass emergency vehicles that are pulled over."
The driver of the striking vehicle has been identified as Zachary A. Morrison, 20, of Frederick, Maryland. Deputies say Morrison stopped at the scene, and cooperated fully with the investigation. No citations have been issued at this time, but the investigation is ongoing.
Morton has been with the agency since December of 2010 and is assigned to the Sheriff's Office Traffic Unit.