Background: An additional shunt in single ventricle patients with Glenn anastomosis may increase pulmonary flow at the expense of ventricle volume overloading. The performance of the modification depends on pulmonary resistance, indicating better results in favorable hemodynamic conditions. Aims: The study aims at analyzing the influence of precisely adjusted pulsatile shunt in borderline high-risk Glenn patients on early and late results. Methods: The study involved 99 patients (including 21 children) with the bidirectional Glenn and accessory pulsatile shunt (BDGS group), and 78 patients with the classic bidirectional Glenn anastomosis (BDG group). Results: There was 1 death in the BDGS group and 4 deaths in the BDG group. No difference in mortality (P = 0.71) was found. The Fontan completion was achieved in 69 (88.5%) children in the BDG group and 18 (85.7%) patients in the BDGS group, without fatalities. No intergroup differences in postoperative pulmonary artery pressure (P = 0.10), ventilation time (P = 0.12), the McGoon ratio (P = 0.9), or chylothorax frequency (P = 0.14) were observed. Intensive care unit (P = 0.28) and hospitalization (P = 0.05) times were comparable. Echocardiography revealed no significant differences in the ventricle and atrioventricular valve function between groups. In the BDGS group, higher blood oxygen saturation (P = 0.03) and increase of the McGoon index (P = 0.002) were noted. Conclusions: Bidirectional Glenn anastomosis with precisely adjusted accessory pulmonary blood flow provides stable hemodynamics and adequate oxygen saturation in borderline, profoundly hypoxic patients. An advantageous pulmonary artery development before Fontan completion was observed.