We present our single-centre results of paediatric patients who underwent surgical atrial septal defect II closure via lateral thoracotomy. Retrospective analysis. Patients were divided into a cardiac arrest group and a cardiac fibrillation group. All procedures were performed via right midaxillary thoracotomy through a single incision without side ports. All 37 consecutive patients between March 2019 and August 2022 (median age 3 years; percentile 25th: 2; 75th: 5 years) in both groups were free of mortality and postoperative morbidity such as haemodynamically relevant residual shunt or malignant arrhythmias. Cardiopulmonary bypass time was significantly shorter in the fibrillation group (mean: 34.7 min vs 52.6 min, P = 0.01), and all patients were weaned off the ventilator immediately postoperatively. Length of the intensive care unit stay was not different between the 2 groups. Postoperative hospital stay was significantly longer in patients with cardiac arrest (mean: 5.6 days vs 4.9 days, P = 0.04). Postoperative laboratory parameters did not differ between the 2 groups. All patients were discharged with normal left ventricular function and normalized cardiac enzymes. Minimally invasive closure of an atrial septal defect during atrial fibrillation is a safe procedure with results comparable to those of an induced cardiac arrest procedure.