Ventricular dyssynchrony is associated with morbidity and mortality after palliation of a single ventricle. The authors hypothesized that resynchronization with optimized temporary multisite pacing postoperatively would be safe, feasible, and effective. Pacing was assessed in the intensive care unit within the first 24 h after surgery. Two unipolar atrial pacing leads and four bipolar ventricular pacing leads were placed at standardized sites intraoperatively. Pacing was optimized to maximize mean arterial pressure. The protocol tested 11 combinations of the 4 different ventricular lead sites, 6 atrioventricular delays (50–150 ms), and 14 intraventricular delays. Optimal pacing settings were thus determined and ultimately compared in four configurations: bipolar, unipolar, single-site atrioventricular pacing, and intrinsic rhythm. Each patient was his or her own control, and all pacing comparisons were implemented in random sequence. Single-ventricle palliation was performed for 17 children ages 0–21 years. Pacing increased mean arterial pressure (MAP) versus intrinsic rhythm, with the following configurations: bipolar multisite pacing increased MAP by 2.2 % (67.7 ± 2.4 to 69.2 ± 2.4 mmHg; p = 0.013) and unipolar multisite pacing increased MAP by 2.8 % (67.7 ± 2.4 to 69.6 ± 2.7 mmHg; p = 0.002). Atrioventricular single-site pacing increased MAP by 2.1 % (67.7 ± 2.4 to 69.1 ± 2.5 mmHg: p = 0.02, insignificant difference under Bonferroni correction). The echocardiographic fractional area change in nine patients increased significantly only with unipolar pacing (32 ± 3.1 to 36 ± 4.2 %; p = 0.02). No study-related adverse events occurred. Multisite pacing optimization is safe and feasible in the early postoperative period after single-ventricle palliation, with improvements in mean arterial pressure and fractional area shortening. Further study to evaluate clinical benefits is required.