Objective To investigate the clinical and genetic characteristics of CDKL5 gene mutation-associated with early-onset epileptic encephalopathy. Methods The clinical characteristics and genetic variation of CDKL 5 gene mutation in a baby boy with early-onset epileptic encephalopathy were analyzed. Results On the 30th day after birth, the children began to have a variety of forms of seizures, such as tonia, spasm, myoclonus, and accompanied by a significant waking athetosis. The child was treated with a combination of antiepileptic drugs with poor efficacy, which resulted in refractory spasmodic seizures, severe developmental delay and language and motor delay. Gene examination revealed a de novo c. 416 A>G (p.Glu 139 Gly) missense mutation in CDKL 5 gene, which has not been reported. Conclusion In this paper, the mutation spectrum of CDKL 5 was expanded (c.416 A>G), which could lead to severe early-onset epileptic encephalopathy in male children.