Sessile hypothalamic hamartoma (HH) often causes intractable epilepsy, which is difficult to control even by microsurgical resection and gamma knife surgery (GKS), especially when the hamartoma is intrahypothalamic, large, or irregularly shaped. We successfully applied radiofrequency ablation (RFA) to reduce its epileptogenicity and to disconnect seizure propagation. The patient was a 26-year-old man who presented with refractory epilepsy and severe mental retardation from age 6 months. He had undergone three surgeries yielding partial resection and conventional irradiation treatments. The residual HH was thin and shaped like a bent plate, attached widely to the floor of the third ventricle. He underwent open RFA via the transcallosal sub-choroidal approach under strict image guidance, which resulted in immediate and remarkable seizure remission without complications. This suggests that open RFA is a minimally invasive technique for an irregularly shaped HH that is difficult to treat by other modalities.