Abstract Background A ketogenic diet (KD) is an effective treatment for intractable epilepsy in children. Protein–losing enteropathy (PLE) is a rarely reported but serious complication of KDs. Case presentation A 3-month-old female patient presented with PLE while following a KD as treatment for intractable epilepsy. She also had genovariation of the STXBP1 gene. The patient suffered from general edema and hypoalbuminemia but no diarrhea. Esophagogastroduodenoscopy (EDG) revealed lymphatic ectasia in the lamina propria. We diagnosed her with intestinal lymphangiectasia, and after decreasing the KD ratio from 4:1 to 1.05:1, we successfully controlled her edema and hypoalbuminemia. As of now, the convulsions and hypsarrhythmia have disappeared, and the seizure-free state has lasted for 20 months. Conclusions PLE may be managed by decreasing the ketogenic ratio rather than discontinuing a KD since for some patients, a KD is the only effective therapy available at present.