Snapping shoulder syndrome could be effectively treated with scapulothoracic arthroscopy. The excision of the scapular superomedial corner is assumed to help lower the recurrence rate. However, the amount of resection is still controversial. Furthermore, we lack a technique to measure if the resected amount was adequate based only on arthroscopy evaluation. We describe a 47-year-old man who suffered from severe snapping shoulder syndrome as a consequence of a deformity of the left superomedial scapular corner. The patient had endoscopic bursectomy and superomedial corner resection. Intraoperative three-dimensional CT scans (3D-CT) were used to evaluate the amount of resection. The patient recovered without incident and resumed his usual activities within 30 days following surgery. At the six-month follow-up, there were no recurrent symptoms. Intraoperative 3D imaging significantly enhances the safety and efficacy of scapulothoracic arthroscopy. This is a novel technique that, to our knowledge, has not been reported previously in the literature. •The scapular superomedial corner excision may help reduce recurrence rates of treatment for snapping shoulder syndrome.•The lack of anatomical landmarks makes estimating the resected volume by arthroscopic vision challenging.•This is the first report of the application of intra-operative 3D imaging for scapulothoracic arthroscopy.•Intraoperative 3D imaging significantly enhances the safety and effectiveness of scapulothoracic arthroscopy.•Intraoperative 3D imaging help in the precise identification of anatomical landmarks in small or complex regions.