Rain Rot is totally a result of a horse running out of stored Vitamin A. That is why they always get it in the winter and early spring before there is good green grass and hay is getting too old to have any Vitamin A left in it.
If a horse has sufficient Vitamin A coming in or stored in their livers, you cannot give them rain rot or lice.
I would think that your horse may have lice instead of rain rot -- but the cure is the same. Rain rot is most frequently seen on the top of a horse and on the areas that rain hits -- which is how it got its name. It also usually has little scabs attached to clumps of hair that come off leaving sores, sometimes bloody, underneath them. It is more often caused by bacteria than fungus and it IS NOT contagious. You just cannot give it to a horse with healthy skin and a good immune system.
Using topicals only temporarily stops it as it comes right back if the horse's diet has not improved to get it more Vitamin A or Beta Carotene that turns into Vitamin A. It is a malfunction of the horse's immune system.
We quit treating it over 40 years ago when I was informed by a very good nutritionist that it was a Vitamin A thing. He was right. Add ing Vitamin A has cleared up 100% of the cases I have had come in ever since.
You can feed a good supplement with a high level of Vitamin A (like Mare Plus made by Farman) or you can 'jump start' the process by giving a horse 5cc of an injectable Vitamin A sold for cattle. You just squirt it in the horse's mouth and DO NOT give it a shot. Do it once a week and you will see rain rot, lice, goopy or crusty eyes and several other things tied in to adequate Vitamin A levels completely disappear.
Several people have come on this forum and told how it worked for them with no messy or expensive topical treatments. We have not treated one in more than 40 years and 100% of them have cleared right up.