HeartMate 3 (HM3) has demonstrated excellent outcomes in adults, and its use in pediatric patients has recently increased. In small pediatric patients, previous studies have mainly focused on whether the device can be accommodated within the thoracic cavity. However, the physiological suitability of pump flow relative to body size and the potential mechanical effects of the device have not been well investigated. A 12-year-old girl (height 138 cm, weight 28.9 kg, body surface area 1.07 m2) with dilated cardiomyopathy and complete atrioventricular block developed progressive heart failure and became catecholamine dependent. HM3 implantation with pacemaker placement was performed. Preoperative pulmonary artery pulsatility index (PAPi) was 2.3, with no obvious right heart failure (RHF). Postoperatively, central venous pressure (CVP) remained elevated at 15-18 mmHg and PAPi decreased to 0.2, indicating severe RHF. Massive left pleural effusion and hypoxemia occurred, and extubation was delayed until postoperative day 7. Lymphangiography and treatment for subclavian vein occlusion did not improve the effusion, suggesting RHF as the primary cause. Adjustment of HM3 pump speed and pacemaker settings during cardiac catheterization reduced CVP and rapidly improved the pleural effusion. In small pediatric patients undergoing HM3 implantation, device-related mechanical effects within the limited thoracic cavity and relatively high circulatory support for patient body size may contribute to RHF even when anatomical accommodation is feasible. Careful optimization of pump speed and heart rate may therefore be important in small pediatric patients.