Ed Smith of the Independent Fire Company said the fire was reported about 4:40 a.m..
Damage to the barns was estimated at about $1.2 million but the value of the horses wasn't known, The (Martinsburg, W.Va.) Journal reported.
While the blaze was to be investigated by a state fire marshal, Smith said it was not believed to have been arson, The Journal said.
The Hagerstown, Md. Herald-Mail reported 25 of the horses died in one barn and two were in another.
Lenny Hale, executive director of the Charles Town Horsemen's Benevolent and Protective Association, said the group was seeking donations to help trainers who lost horses.
"We haven't had the best day here, but it could have been a lot worse if it had been windy and it spread faster," Hale said. "But we've gotten an overwhelming amount of support."