Despite many different medications, 30% of epileptic patients remain drug-resistant, in particular those with mesial-temporal lobe epilepsy (MTLE). MTLE is characterized by focal seizures arising in the temporal lobe, and is associated with hippocampal sclerosis in 80% of patients, as well as with several cognitive and emotional comorbidities. Resection of the epileptogenic zone, although effective, is very invasive, risky and generates side effects. To develop a non-invasive and effective treatment, we evaluated the therapeutic potential of synchrotron-generated X-ray microbeams, an innovative approach called Microbeam Radiation Therapy (MRT), previously developed in neuro-oncology. MRT allows for targeting a precise brain region, sparing normal tissues and with limited side effects. We sought to determine the optimal protocol of MRT to abolish focal seizures in a mouse model of MTLE obtained by intrahippocampal injection of kainate. To this aim, in KA-MTLE mice with recurrent focal seizures and MRI-validated hippocampal sclerosis, we performed irradiation of the epileptogenic zone using 1, 3 or 5 equidistant ports at doses of 125, 250 and 500 Gy (5 parallels microbeams 50 μm wide, 400 μm apart). Multiport MRT had sustainable antiepileptic effects over 8 months, in particular with 5 ports, as measured by electroencephalographic recordings. MRI and histological analysis indicated a high tolerance of healthy tissues, whereas behavioral tests indicated limited changes in cognitive or emotional comorbidities. Our data suggest that MRT should be an effective non-invasive way to treat focal drug-resistant epilepsies, with limited side effects compared to resective surgery or gamma knife irradiation.