We encountered a rare case displaying pathological changes resembling bone cyst of the lateral tibial subchondral bone following arthroscopic partial meniscectomy for discoid lateral meniscus in a boy. Differentiating between bone tumor and osteochondritis dissecans was difficult. Moreover, since an epiphyseal line was remained, deciding on the appropriate medical treatment was also troublesome. However, we selected operative therapy. As the result, an excellent clinical outcome was obtained without damaging the epiphyseal line. We report the analysis of mechanisms causing of this pathological change and the treatments used, with some references to the literature.