A 15-year-old female patient was admitted to the hospital due to developmental retardation for 14 years and significant motor and cognitive regression for more than 1 year. The clinical features of this patient were myoclonus, intention tremor, ataxia, tendon hyperreflexia, hypertonia, dysarthria, speech regression, intellectual disability and multifocal seizures. Electroencephalogram showed typical epileptic discharge and the epilepsy was refractory. The patient had developmental retardation since childhood. Walking gait instability gradually aggravated, and eventually developed into walking difficulties with tremor of limbs. In addition of seizures, language and cognitive regression of the patient was evident. Genetic testing found a variation of SEMA6B gene in the child, which was determined as a pathogenic variation combined with genetic characteristics and clinical phenotype, and the child was diagnosed as progressive myoclonic epilepsy (PME). Treatment of PME is generally anti-seizure, as well as palliative support and rehabilitation measures. Most patients have poor prognosis. Genetic testing contributes to the diagnosis and treatment of patients with refractory epilepsy. SEMA6B gene variation can lead to PME phenotype. The gene variation C.2149 (exon17) C>T has not been reported before, which expands the gene variation spectrum of PME.