Objective To explore the clinical characteristics and gene mutation of primary congenital lymphedema (PCL). Method The clinical data and gene test results from a PCL child and his parents were retrospectively analyzed and relevant literature were reviewed. Results The boy had a full-term natural birth. Right pleural effusion was found before and after birth, accompanied by pericardial effusion, pleural effusion and edema of lower limbs. A novel heterozygous mutation of c. 3820 G > A (p.Asp 1274 Asn) inherited from his father was found in FLT 4 gene by gene detection. His father also had edema in both lower limbs after birth, which was gradually self-healing. Conclusion For children with congenital edema, it is necessary to pay attention to the family history and genetic testing could be performed to find the PCL and other congenital lymphatic dysplasia of the newborn.