BACKGROUND Abnormalities in the melanocortin receptor 4 (MC4R) gene often lead to obesity, but are rarely associated with other conditions such as epilepsy and sleep disorder. CASE SUMMARY Here, we present a case of a male obese child with a heterozygous variant in MC4R (c.494G>A, p.Arg165Gln) inherited from his father, who presented with disordered sleep and abnormal facial movements. Examination through melatonin rhythm testing and electroencephalography led to a diagnosis of sleep disorder and epilepsy, as his melatonin rhythm was markedly distorted and the electroencephalography revealed epileptic discharges. He received treatment with an antiepileptic drug; however, the therapy was ineffective and the sleep disorder appeared to be deteriorating. Subsequently, we initiated adjuvant treatment with melatonin. Upon re-examination, his body mass index had decreased, the sleep disturbance had resolved, and his seizures were well controlled. Electro-encephalography review was normal, and a typical melatonin rhythm was restored. CONCLUSION We concluded that, in addition to causing obesity, abnormalities in the MC4R gene may contribute to the development of sleep disorders and epilepsy, and that melatonin can be used as an adjuvant therapy to alleviate these symptoms.