CYP21A2 mutation is the major cause of Congenital Adrenal Hyperplasia (CAH) resulted from the defect in 21-hydroxylase. In this study, we reported a patient of CAH with an unusual mutation of CYP21A2 gene. This patient was a six-year-old girl admitted to Huai’an First People’s Hospital for surgery because of malformation of external genitalia. DNA sequence analysis of CYP21A2 revealed the compound heterozygous mutations (g.6119T>A and g.6699delA) in this patient and her elder sister. Interestingly, the g.6119T>A mutation is associated with a Simple Virilizing (SV) phenotype of CAH, and the g.6699delA is a rare mutation that has not been reported so far. This case report of the patient with an unusual SV CAH identified a previously unreported mutation of the CYP21A2 gene, thus enlarging the spectrum of known mutations related with CAH. DNA sequencing of the CYP21A2 to identify rare mutations should be used for the genetic diagnosis and genetic counselling of CAH.