Many stores that offer horse care supplies will offer tools you can use to help ward off annoying flies from your horse. If your horse is having trouble with flies, you might consider investing in a fly mask. These lightweight masks protect your horse's eyes from flies. You can also find models that protect its ears and jowls.  Place insect traps around the areas your horse lives and spends time in during the day. From chemical fly repellents to products that encourage natural fly predators, you have plenty of options to help decrease the number of irritating and potentially disease-carrying flies that pester your horse. To cut down on fly problems, make sure the horse's stable and the building you keep your horse is regularly cleaned. Allowing waste and droppings to build up will attract more flies.