Current dosing guidelines for unfractionated heparin therapy in pediatric patients are based on recommendations of only one study that evaluated a weight-based dosing nomogram. To test the hypothesis that adhering to a strict weight-based nomogram yields better therapeutic results in pediatric patients, we prospectively monitored 25 consecutive pediatric patients who received unfractionated heparin based on the nomogram, and compared them to control patients whose treatment did not follow the standard nomogram. The mean time needed to achieve the target activated partial thromboplastin time was significantly shorter in the study group than the control group (18.32 ± 9.98 vs. 43.8 ± 30 h). A higher proportion of the study group reached the target activated partial thromboplastin time at 12, 24, and 36 h, compared to controls: 44% vs. 6%, 72% vs. 28%, 100% vs. 58%, respectively. Within the study group, patients under 1 year of age needed more time to achieve the target activated partial thromboplastin time than those over 1-year old. The performance of the standard dosing nomogram was excellent with regard to early anticoagulation target achievement, without increasing the risk of bleeding. Further studies are warranted to refine this nomogram for pediatric patients who are less than 1-year old.