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Subchondral bone cysts are intraosseous cystic lesions typically associated with degenerative joint diseases in weight-bearing joints; however, their occurrence in the humeral trochlea is extremely rare. We report a case of a 19-year-old Japanese archer who presented with a 2-year history of right elbow pain. CT revealed an 8- × 4- × 4-mm cystic lesion with partial disruption of the subchondral bone plate on the lateral aspect of the humeral trochlea. As arthroscopic access is technically challenging and intra-articular curettage through the joint surface would damage the cartilage, a navigation-assisted extra-articular approach was selected. A patient-specific three-dimensional surgical plan was designed to achieve cylindrical excision of the lesion and was reconstructed with a β-tricalcium phosphate bone substitute. Postoperative CT scans confirmed complete removal of the cyst. Postoperatively, the patient's elbow pain gradually improved and had completely resolved at 14 months. This case demonstrates that navigation-assisted extra-articular curettage is a feasible technique for treating deep subchondral bone cysts of the humeral trochlea while preserving the articular cartilage.