Epilepsy surgery is a common therapeutic option in humans with drug-resistant epilepsy. However, there are few reports of intracranial epilepsy surgery for naturally occurring epilepsy in veterinary medicine. A 12-year-old neutered female domestic shorthair cat with presumed congenital cortical abnormalities (atrophy) in the right temporo-occipital cortex and hippocampus had been affected with epilepsy from 3 months of age. In addition to recurrent epileptic seizures, the cat exhibited cognitive dysfunction, bilateral blindness, and right forebrain signs. Seizures had been partially controlled (approximately 0.3–0.7 seizures per month) by phenobarbital, zonisamide, diazepam, and gabapentin until 10 years of age; however, they gradually became uncontrollable (approximately 2–3 seizures per month). In order to plan epilepsy surgery, presurgical evaluations including advanced structural magnetic resonance imaging and long-term intracranial video-electroencephalography monitoring were conducted to identify the epileptogenic zone. The epileptogenic zone was suspected in the right atrophied temporo-occipital cortex and hippocampus. Two-step surgery was planned, and a focal cortical resection of that area was performed initially. After the first surgery, seizures were not observed for 2 months, but they then recurred. The second surgery was performed to remove the right atrophic hippocampus and extended area of the right cortex, which showed spikes on intraoperative electrocorticography. After the second operation, although epileptogenic spikes remained in the contralateral occipital lobe, which was suspected as the second epileptogenic focus, seizure frequency decreased to <0.3 seizure per month under treatment with antiseizure drugs at 1.5 years after surgery. There were no apparent complications associated with either operation, although the original neurological signs were unchanged. This is the first exploratory study of intracranial epilepsy surgery for naturally occurring epilepsy, with modern electroclinical and imaging evidence, in veterinary medicine. Along with the spread of advanced diagnostic modalities and neurosurgical devices in veterinary medicine, epilepsy surgery may be an alternative treatment option for drug-resistant epilepsy in cats.