The preterm and term neonatal population is most at risk for thrombotic complications in pediatrics. Among various treatment modalities, anticoagulation is primarily used in the management of thrombosis. Developmental differences in preterm and term infants compared to older infants and children and limitations of anticoagulation agents currently used are important considerations for treatment. Additionally, dosages and durations of anticoagulant treatment are widely variable across countries. This article will highlight the differences in anticoagulation in neonates compared to other populations due to developmental hemostatic changes, epidemiology of neonatal thrombosis, pharmacokinetic and pharmacodynamic properties of drugs used and presence of neonatal co-morbidities.