Although neurobeachin (NBEA) de novo genetic variants have been mainly reported in patients with neurodevelopmental disorders (NDD), they have also been recently associated with early childhood epilepsy. We report an 11-year-old boy who was first evaluated at 34 months of age because of drug-resistant epileptic encephalopathy. He also had developmental delay and prominent autistic features. Whole-exome sequencing (WES) disclosed a pathogenic NBEA c.5258_5279del, p.(Ala1753Valfs*13) variant, occurring de novo and a paternally-inherited heterozygous NBEA c.416T>C p.(Met139Thr) variant of uncertain significance (VUS). The patient showed good response to the ketogenic diet, suggesting that this therapy may be an effective option for patients with seizures who carry NBEA variants.