Variants in the X-linked gene PCDH19 are associated with early infantile epileptic encephalopathy-9 (EIEE9) characterized by early onset of variable types and frequency of recurrent cluster of seizures, mild to severe intellectual disability, autistic traits, psychiatric features, and behavioral problems. The disorder affects heterozygous female and mosaic male patients. Until now, only twelve affected mosaic male patients have been reported in literatures. Here, we report a 3.5-year-old male patient who had epileptic seizures at the age of 1.5 years, but had relatively normal cognition competence and developmental milestones. Whole exome sequencing revealed a de novo mosaic hemizygous missense mutation in PCDH19 [c.*G>A (p.Glu*Lys)] and the percentages of mosaicism is about 90%. The other case is 2-year-old female who presented with infantile epileptic encephalopathy, delayed development, developmental regression and moderate cognitive impairments. Whole exome sequencing revealed a de novo heterozygous missense variant in PCDH19 for c.*G>C (p.Asp*His). The two novel missense muations in this study have never been reported. In vitro studies demonstrated that the two novel missense variants induced a decrease in PCDH19 protein expression which further showed pathogenic nature. Our work not only expands the mutant spectrum of the PCDH19 gene but also provides new insights on its resulting phenotype.