Hope, a tabby-and-white kitten, was found with no internal or external sex organs after they were examined at a Cats Protection centre in Gateshead.
Animal officers said there was no term for the cat's condition because it was so rare but added it had been "exciting to discover Hope's special status".
The charity added the 15-week-old pet was healthy and ready to be rehomed.
Hope was originally thought to be a female cat when it was handed in by a family to Cats Protection's rescue centre in Warrington, but vets found no external sex organs.
Cats Protection's senior field veterinary officer Fiona Brockbank said it appeared to be a case of agenesis, the failure of an organ to develop, which she and her colleagues had never seen before.