Pediatric cardiothoracic surgery is often associated with low cardiac output in the postoperative period. This study sought to determine whether increasing heart rate via temporary atrial pacing is beneficial in augmenting cardiac output. Patients younger than 18 years who underwent cardiothoracic surgery and had no perioperative arrhythmias were eligible for the study. Patients not paced postoperatively were atrial paced at a rate of 15 % above the intrinsic sinus rate (not to exceed 170 beats per minute, less for older patients) for 15 min. Patients paced for cardiac output postoperatively had their pacemakers paused for 15 min. Markers of cardiac output were measured before and after the intervention. Of the 60 patients who consented to participate, 30 completed the study. Failure to complete the study was due to tachycardia (n = 13), lack of pacing wires (n = 7), junctional rhythm (n = 4), advanced atrioventricular block (n = 3), and other cause (n = 3). Three patients were paced at baseline. There was no change in arteriovenous oxygen saturation difference, mean arterial blood pressure, central venous pressure, toe temperature, or lactate with atrial pacing. Atrial pacing was associated with a decrease in head and flank near-infrared spectroscopy (p = 0.01 and <0.01 respectively). Secondary analysis found an inverse relationship between mean arterial pressure response to pacing and bypass time. Temporary atrial pacing does not improve cardiac output after pediatric cardiac surgery and may be deleterious. Future research may identify subsets of patients who benefit from this strategy. Practitioners considering this strategy should carefully evaluate each patient's response to atrial pacing before its implementation.