How to humanely kill a squirrel in a cage
A squirrel infestation at home can be a nuisance at best and a health hazard at worst. Killing a squirrel can never be entirely humane, but there are measures to take to cause as little suffering as possible. There are relevant questions about legality, so you should check the law in your state before proceeding. Definitions of humane and cruel may vary, but there are some general guidelines to keep in mind. If you have a live squirrel in your home to dispose of, consider these humane options.
Using asphyxiation by CO2
Asphyxiation by CO2 is the only approved method by the American Veterinary Medical Association to get rid of squirrels and other rodents, which makes use of common household materials. These guidelines are meant for veterinarians, not ordinary folks. You should think about whether you are qualified to carry this out without causing undue pain and suffering for the squirrel. It is not easy or straightforward, but when done appropriately, it is considered the most humane. As a general rule, it is best to take the squirrel to your vet.
Killing the squirrel with blunt force trauma to the head
The goal of this method is to destroy the squirrel’s brain with one swift, forceful blow to the head from a blunt hammer or another hard striking object. This approach can be daunting and emotionally taxing. If you have any reservations about whether you can kill the squirrel in one blow, seriously consider other options. There is a risk of causing much more pain and distress if you carry this out in the wrong way. Confine the squirrel, in one corner of a sturdy sack or bag before striking, to ensure you have a clear shot. Avoid smashing it against a wall or stomping it haphazardly, as this can result in a painful and protracted death for the squirrel.
Using spring traps
A sturdy and re-usable spring trap is still considered to be the most humane of the various traps. Spring traps also cause pain to squirrels caught in them, but they should kill the squirrel very quickly. There are designs and set-up tactics to ensure these traps make a quick death more likely.

Placing the trap at right angles to a wall, ensuring that the rest of the trap is clean, and making sure the squirrel has a clear path to the trap will make it more probable that, when tripped, the trap will fully close and the squirrel will be killed rather than injured.
Shooting the squirrel
This method should only be carried out by someone skilled with a gun, and even then, the probability of a shot that instantly kills the squirrel is small. It is advisable to use a low power air gun to avoid causing a bigger mess and spreading biological matter. A gunshot to the head should kill the squirrel instantly. Killing the captured squirrel in the cage is the way to go. The shooting environment should be prepared carefully because chances are that the bullet will pass through the head of the squirrel, and may hit any object behind it.
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