Congenital nephrotic syndrome (CNS) refers to a disease presenting with massive proteinuria in association with hypoalbuminemia, hyperlipidemia, and edema at birth or within the first three months of life. In the past, most children with CNS had extremely poor prognosis and succumbed to various complications, usually within the first 6 months. Recent advancements in protein supplementation and nutritional support, renal replacement therapy and renal transplantation in infancy, render these patients to have much better outcomes [1-5]. However, there are still many hurdles in the management of this disease. Thromboembolism is an uncommon, yet important complication which the healthcare givers must be aware of. This article reviews the challenges in the management of the thrombotic complications with special emphasis on the unique characteristics of the newborn hemostasis system and anti-thrombin (AT) depletion in nephrotic syndrome. Due to the relatively low incidence of CNS in children and scarce information in the literature on the optimal management of the thromboembolic complications, most of the recommendations are based on the authors’ experience.