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How to Debug a Squirrel

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While parasites plaguing squirrels may  make us cringe, keep in mind they are the very same infecting our dogs and cats, and we manage to handle their care just fine.


Many treatments available for pets are safe for squirrels.  A good rule of thumb is: if it's safe for pet rodents, its safe for squirrels. The difference to be mindful of when handling these animals is that squirrels are wild prey species and we are predators - which makes our handling of them much more stressful for them than with our pets.

Below you'll find information about diseases that come from parasites, types of parasites, and ways to safely debug a squirrel infected with those parasites.

Vector Borne Diseases


In biological terms, vectors are organisms that carry diseases to other organisms. Any animal, domestic or wild, can be infested with ectoparasites such as fleas, ticks, mites, flies, and other nasty vermin that can act as vectors - spreading disease from animals to people (zoonotics). Fleas, ticks or any other parasite that feeds on blood from its host can ingest infected blood and transmit that infection to a new host when dining on their next prey.  

To ensure that next prey isn’t you, your family or pets, all ectoparasites must be removed as soon as possible and any bedding or materials the animal has been in contact with washed in hot water with detergent and dried in a hot dryer, or discarded.  

Safe Ectoparasite Removal

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Fleas, Ticks & Mites

If the squirrel has little or no hair then simply brush off any parasites and flush them down the drain with hot water.  

If the squirrel is furred it’s safe to treat with any flea medication safe for kittens such as a flea spray, powder, dip or shampoo.  If you do wash the baby, ensure the water is warm, the shampoo is thoroughly rinsed off and the baby dried completely. Take care to keep all chemicals out of eyes and nose.

Capstar® is a pill that can be administered topically or orally.  It can be crushed and dissolved in water as a spray, or 1/5 pill crushed  and added to a fluid given by mouth.  Capstar pill will kill adult fleas.  

Revolution®/Stronghold® (generic selamectin) or Advantage® on the back of the neck will offer longer term results and kills a much broader variety of parasites. Both are safe and effective treatment for squirrels.

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Remove any larvae you can see by brushing them off. Thoroughly flush the wound with saline solution (such as you would use to clean contact lenses) or warm water.


To ensure there are no internal larvae, cover the wound with a thick layer of triple antibiotic ointment or lubricant (such as KY Jelly) and watch closely for movement as any larvae attempts to breakthrough to breath.  As each raises its ugly head out of the opening, grab it with tweezers and pull it out. Repeat until you see no movement from the wound.  All larvae must be removed or the animal will die. 


Fly Eggs

Fly eggs look like small grains of white rice. These can be brushed off or washed off with flea shampoo.  Make sure that you check within the ears, mouth, eyes, genitals, anus and in between folds of skin.

Safe Endoparasite Removal

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All animals can get worms, including squirrels.  Usually it is not necessary to deworm squirrels unless you have some reason to believe the animal is infected, such as a failure to gain weight or if you witness a little visitor waving at you from an orifice down under.   As nasty as this is, most worms are quickly and easily dispatched with fenbendazole available at most pets stores. Dosage is 20 to 50 mg per kilogram (or 2 to 5 mg per 100 grams weight) once per day for three days.  

Squirrel Care Resources


Learn about common squirrel illnesses that could be plaguing your baby.


Learn how to treat injuries in need of immediate care before transport.


Find out what to feed a squirrel, how much and how often.


Find out what it takes to house a squirrel and keep them safe.

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