She was initially refused service while in the saddle in the drive-through lane of the branch in Whitefield, Greater Manchester.
She then led the animal inside, where it defecated on the floor.
Police were called to the restaurant in Bury New Road on Saturday.
A statement posted on the Facebook page of Greater Manchester Police’s Whitefield Division read: “The staff refused to serve the women due to company policy. The woman then took the horse into the restaurant, who ended up doing his business on the floor.
“The sight and smell of this caused obvious distress and upset to customers trying to eat, as well as staff members.
“Officers arrived at the location and a woman was issued a fixed penalty notice for causing alarm and distress to other customers and staff.”
A spokeswoman for McDonald’s said: “I can confirm that on 20th July a woman allowed her pony to enter our restaurant in Whitefield after being refused service in the drive-through lane.
“The health and safety of our customers and staff is our top priority and for this reason we are unable to serve pedestrians, bicycle riders or customers on horseback through the drive-through.”