The safety and efficacy of selective antegrade cerebral perfusion (SACP) in children undergoing aortic arch surgery are unclear. In this retrospective analysis, we compared moderate hypothermic circulatory arrest (MHCA; n = 61) plus SACP vs deep hypothermic circulatory arrest (DHCA; n = 53) in children undergoing aortic arch surgery during a period from January 2008 to December 2017. Demographic characteristics and the underlying anomalies were comparable between the two groups. The MHCA + SACP group had shorter cardiopulmonary bypass (CPB) time (146.9 ± 40.6 vs 189.6 ± 41.2 min for DHCA; p < 0.05) and higher nasopharyngeal temperature (26.0 ± 2.1 vs 18.9 ± 1.6 °C; p < 0.01). The MHCA + SACP group had lower rate of neurologic complications (3/61 vs 10/53 for DHCA; p < 0.05) but not complications in other organ systems. The MHCA + SACP group also had less 24-hour chest drainage (median, interquartile rage: 28.9, 12.6–150.0 vs 47.4, 15.2–145.0 ml/kg for DHCA; p < 0.05), shorter duration of postoperative mechanical ventilation (35.0, 15.4–80.3 vs 94.0, 42.0–144.0 h; p < 0.01), and shorter stay in intensive care unit (3.9, 3.0–7.0 vs 7.7, 5.0–15.0 d; p < 0.05). In regression analysis, in-hospital mortality was associated with longer CPB time. In conclusion, MHCA + SACP is associated with better short-term outcomes in children receiving aortic arch surgery under CPB.