Background Jansen-de Vries syndrome is a rare autosomal dominant neurodevelopmental disorder caused by pathogenic variants in the last and penultimate exons of the PPM1D gene. It is characterized by delayed psychomotor development, intellectual disability with speech delay, behavioral abnormalities, and dysmorphic features. Up to date, only 17 affected patients have been reported worldwide (no report in Chinese). Methods Here, we analyzed the clinical data and genetic test results of a Chinese patient with Jansen-de Vries syndrome admitted in our hospital in May 2019. Results We report a 9-month-old boy carrying a pathogenic variant (c.1254_1255del, p.(V419Qfs*14)) in PPM1D exon 5, which can account for his phenotype. Most of his clinical features overlap with the reported phenotype, such as growth retardation, feeding difficulties, constipation, congenital abnormalities (such as atrial septal defect, ventricular septal defect, and patent ductus arteriosus), small hands and feet with broad forehead, low-set posteriorly rotated ears, wide mouth with thin upper lip and pointed chin; however, he also presented with additional features like hepatomegaly and left inguinal hernia. Conclusion This is the first published case of Jansen-de Vries syndrome in Chinese population, which will help us to enrich the clinical spectrum of this syndrome.