Abstract Background Right lateral thoracotomy is increasingly used because of its cosmetic benefits, shorter hospital stays, rapid return to full activity, and ease of reoperation in pediatric patients with uncomplicated congenital heart disease. Currently, one-lung ventilation (OLV) is used in these children to facilitate surgical exposure. We aimed to assess the effect of OLV on postoperative outcomes. Methods Children aged 6 months to 6 years undergoing right lateral thoracotomy cardiac surgery with cardiopulmonary bypass (CPB) were randomized into an OLV group or a control group. For the OLV group, the tidal volume was 5 ml/kg with 6 cmH₂O positive end-expiratory pressure from the incision until the end of CPB, whereas patients in the control group received two-lung ventilation, except during vena cava occlusion. Lung ultrasonography was performed twice in the supine position for each patient: first, 3 min after intubation before surgery (T1), and second, 3 min after lung recruitment maneuvers at the end of surgery (T2). The primary outcome was the incidence of postoperative pulmonary complications within 72 h of surgery and significant atelectasis (defined by a consolidation score of ≥ 2 in any region) at T2. Results Overall, 54/96 (56.3%) children developed postoperative pulmonary complications after lateral thoracotomy cardiac surgery with CPB. The incidence of postoperative pulmonary complications was 52.1% (25/48) and 60.4% (29/48) in the OLV and control groups, respectively (odds ratio: 0.712; 95% confidence interval: 0.317–1.600; p = .411). At the end of surgery, the incidence of significant atelectasis was 37.5% in the OLV group compared to 64.6% in the control group (odds ratio: 0.329; 95% confidence interval: 0.143–0.756; p = .008). The consolidation score of the left lung (dependent lung) in the OLV group was significantly lower than that in the control group (p = .007); there was no significant difference in the right lung's postoperative consolidation score between the two groups (p = .051). Conclusions There was no significant difference in the incidence of postoperative pulmonary complications within 72 h of surgery between the two groups. However, children who underwent right lateral thoracotomy cardiac surgery with CPB in the OLV group showed a low incidence of atelectasis at the end of surgery. Trial registration ChiCTR, ChiCTR2100048720. Registered on July 13, 2021, www.chictr.org.cn .