Squirrels are prone to skin parasites such as lice, fleas, ticks, mange and other mites. Wildlife rehabilitators deal with this issue on a regular basis. But even when you purchase your squirrel from a pet store or breeder, you can find these pests on your baby.
The first step in treatment is to figure out exactly how old your infant squirrel is. Every species has a slightly different maturation timeline, but Eastern gray squirrels -- those ubiquitous neighborhood creatures we simply call "squirrels" -- start to grow hair at 2 weeks of age and are fully furred by 5 weeks.
If an infant squirrel is still hairless, hold him gently and use a soft cloth or tissue to simply brush the parasites off his skin into the sink. Then run hot water to kill and flush the bugs down the drain. Place a drop of kitten-safe flea-and-tick medication on the baby's bedding, near the edge, and put him with his face at the other end, away from the medication. If your baby is especially active and moves around a lot, remove the medicated bedding or cover it with another layer.
Treat fully furred squirrels over 5 weeks old with flea medication that's safe for kittens or birds. Choose drops, powder, spray, dip or shampoo.
The easiest method is to use flea and tick drops. Put a single drop on the back of a baby squirrel's neck.
If you choose a spray, spray the medication on a cotton ball rather than directly on the animal. Wipe it gently over his body, starting from the ears so the parasites won't escape into them. Avoid his eye area.
If you choose a shampoo, wash the squirrel in warm water only -- not hot or cold -- and make sure soap doesn't get in his eyes or nose. Then rinse and dry him thoroughly, using a towel or blow-dryer on low setting.
Internal treatments are a little trickier and more involved than external ones, since it's important not to overdose your baby squirrel. If you prefer this course of action anyhow, you can crush a flea-fighting pill that's safe for kittens, mix a fifth of the powder with water, and give it to your squirrel orally with a syringe or eyedropper. You can also dissolve the powder in water and spray it on the squirrel's skin.
A vet might treat mange mites in a baby squirrel with a very small amount of Ivermectin, a veterinary parasite medicine. Baby squirrels are almost impossible for a novice to treat effectively since the dose is so small. Only a vet should make the determination to treat an infant this way.