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Dealing with a pest animal that you have successfully trapped in a cage will often be the most unpleasant part of the process, but even though you may have to kill the animal, you shouldn't make it suffer as well. The key part of dealing with a skunk, or any other pest animal humanely, is to ensure that you kill it in a swift and painless method that will not leave the animal suffering for a long time. It is also worth thinking whether you have any other alternatives to killing the animal, and to see what the regulations are in your area.
When looking at this method of dealing with a skunk, there are several factors to consider. Firstly, when you are shooting the skunk in the cage,you are going to be likely to kill the animal, but you are also likely to blast a hole in the cage. There are also prohibitions on discharging firearms in urban areas, meaning this isn't always an option that is available, while the other option is to let the skunk go and shoot it outside the trap, but you need to be very confident in your shot to do this successfully.
Depending on where you are located, a lethal injection can sometimes be administered by a veterinarian or your local animal services department, and will ensure the skunk dies swiftly and in relatively little pain. The difficulty is that it isn't always going to be available, while preventing the skunk from spraying is very difficult with this method.
Often the easiest method to carry out at home, placing a plastic cover over the cage that is airtight, and then running a vehicle's exhaust emissions into the cage will kill the skunk, almost without it realizing. The build up of carbon monoxide will lead to the animal becoming lethargic and then passing out after just a few minutes, and you shouldn't need to run the engine for more than fifteen minutes to euthanize the skunk in this way.
Can You Consider Relocation?
While killing a skunk can be done humanely, it is worth considering to see if you area does allow the relocation of pest animals, and whether or not there are suitable spots within a short drive away. The benefit of this, if you can find a nice wooded area in which to release the skunk, is that you then do not have to deal with the animal's carcass. For more information, you may want to click on one of these guides that I wrote:
How much does skunk removal cost? - get the lowdown on prices.
How to get rid of skunks - my main skunk removal info guide.