Background Complete atrioventricular canal is a congenital heart defect that is characterized by an atrial septal defect, ventricular septal defect, and a common atrioventricular valve. Standard surgical techniques for repairing complete atrioventricular canal defect mainly includes repairing the defect with a single patch, a double patch, or with the modified single patch technique. Case presentation This paper presents a novel surgical repair technique of an unusual anatomical presentation for a complete atrioventricular canal defect in a patient with Down syndrome. Conclusions Unusual anatomical variant for congenital heart defects occurs frequently, which gives surgeons real opportunities to innovate surgical approaches. This patient was an example of an unusual anatomical presentation for complete atrioventricular canal, and the surgical technique used for this patient was novel. Follow up for these patients is mandatory for long term results.