Background Aggressive treatment of sternoclavicular joint (SCJ) infection involves systemic antibiotics, surgical drainage and resection if indicated. The purpose of this paper is to describe a classification of post resectional SCJ defects and highlight our reconstructive algorithm. Defects were classified into A, where closure was possible often with the aid of topical negative pressure dressing; B, where parts of the manubrium, calvicular head, and first rib were excised; and C, where both clavicular, first ribs and most of the manubrium were resected. Methods Twelve patients (age range, 42 to 72 years) over the last 8 years underwent reconstruction after SCJ infection. There was 1 case of a type A defect, 10 type B defects, and 1 type C defect. Reconstruction was performed using the pectoralis major flap in 6 cases (50%), the latissimus dorsi flap in 4 cases (33%), secondary closure in 1 case and; the latissimus and the rectus flap in 1 case. Results All wounds healed uneventfully with no flap failure. Nine patients had good shoulder motion. Three patients with extensive clavicular resection had restricted shoulder abduction and were unable to abduct their arm past 90°. Internal and external rotation were not affected. Conclusions We highlight our reconstructive algorithm which is summarised as follows: for an isolated type B SCJ defect we recommend the ipsilateral pectoralis major muscle for closure. For a type C bilateral defect, we suggest the latissimum dorsi flap. In cases of extensive infection where the thoracoacromial and internal mammary vessels are thrombosed, the pectoralis major and rectus abdominus cannot be used; and the latissimus dorsi flap is chosen.