Why is my female cat having brown, smelly discharge from her vagina?

As your cat is spayed, it is possible that the discharge you are seeing is coming from the urethra rather than the vagina as both open up into a common vestibule in the body. Dark brown secretions may indicate blood or infection in the urine, and bringing in a sample of your cat's urine to your local vet can be used to determine if this is the case. You may see other signs of illness such as more frequent trips to the bathroom, attempting to go without success, yowling, or pain and irritation. Infections are usually treated with a round of antibiotics as well as switching to a urinary friendly diet. Increasing your cats water consumption will also help reduce further infections.

In some very rare cases, part of the uterus can be left behind during a spay which may become infected. Signs of infection include swelling of the abdomen, extreme pain and lethargy, and greenish or yellow discharge in addition to other possible discharge. This is a serious condition which should be seen by a veterinarian immediately.