Background: The newborn malformation of Primary Lymphatic Dysplasia (PLD), developed primarily due to PIEZO1 gene autosomal recessive mutation, is known to hinder with the lymphatic system action, causing chyle or lymph effusion into the peritoneal cavity or pleura. Case presentation: A 4 years old male subject presented with a recurrent chylothorax and bilateral lower limb edema that started at age of 6 months. Lymphoscintigraphy showed lymphangiectasia with chylothorax. The whole exome sequence consisted of pathogenic variants in PIEZO1 gene associated with Lymphatic Malformation type 6 (LMPHM6). Conclusion: This is the first reported pediatric case of PIEZO1 gene mutation in Saudi Arabia. This case highlighted the wide differential diagnosis of recurrent chylothorax and lower limb edema, as well as the relative literature on the molecular foundation, clinical scale, pathophysiology, and lymphatic malformation treatment. Patients can be improved via application of standardized chylothorax and lymphedema therapies. Overall, awareness of the diseases related to the thoracic lymphatic circulation should be observed as its prognosis may highly promote better approaches for its management.