Background: Prolonged pleural drainage after the Fontan procedure is a common complication. Various protocols have been described, but there is no definitive consensus for the treatment of this complication. Materials and Methods: Our primary aim was to determine the effect of the protocol on the duration of drainage and hospital stay. Our secondary aim was to determine parameters affecting prolonged drainage after the Fontan procedure. Ninety two consecutive patients who underwent the Fontan operation retrospectively analyzed. A protocol-based postoperative management was adopted at July 2018. Patients operated before the protocol were defined as Group 1(n=48), and patients operated after the protocol were defined as Group 2(n=44). Results: The mean age was 5(IQR 4.0-6.9) years the mean body weight was 17.3 (IQR 15.1-21.8) kg.There were statistically significant differences between groups in terms of total drainage, duration of pleural drainage, prolonged drainage and, LOHS(p=0.05,p=0.04, p=0.04,p=0.04,respectively). In the multivariate analysis, the application of the protocol was observed to be the only factor for prolonged drainage (OR:2.46, 95% CI Lower-Upper:1.03-5.86,p=0.04). Conclusion: Standardization and strict application of the medical treatment within a specific protocol without being affected by doctor, nurse or patient-based factors increases the success. After the changes in our medical management strategy, along with the decrease in total drainage and duration of pleural drainage, LOHS was also reduced, of course together with a reduction in the cost. Key Words: Fontan, pleural drainage, hospital stay, protocol