Femoral vein access is the first choice for percutaneous atrial septal defect closure, and when it cannot be used due to anatomic reasons, the alternative sites should be considered, frequently increasing the complexity of the procedure. Here we report the case of a 3-year-old boy, with situs inversus and dextrocardia, electively referred for percutaneous closure of an ostium secundum atrial septal defect. During the procedure, agenesis of the infra-hepatic segment of the inferior caval vein was diagnosed, and no double inferior caval vein or right superior caval vein were identified by ultrasound or angiography. Therefore, we opted to perform the procedure through the left internal jugular vein, with fluoroscopy and transesophageal echocardiographic guidance. Catheters were navigated through a hydrophilic guidewire, and a Stiff guidewire was positioned in the left ventricle for better support. An Amplatzer septa occluder 19 was successfully deployed without major difficulties and the patient was discharged after 24 hours in good clinical condition. Percutaneous atrial septal defect closure through alternative access sites, especially in the presence of situs inversus, may pose significant challenges to the interventional team. In this case, the left internal jugular vein has shown to be a feasible option, allowing the navigation and manipulation of devices without complications. Provided the expertise of the interventional team, and awareness of the risks involved, alternative access sites can be successfully used for paediatric structural interventions.