We designed and evaluated a modified cyst index using the Picture Archiving and Communication System software for treating simple bone cysts of the proximal humerus by preventive intramedullary flexible nail insertion in symptomatic children or adolescents. From January 2007 to December 2009, cases with a cyst index of at least 4 were enrolled in the study. Of 20 total cases, 19 were prospectively followed-up for at least 2 years. The mean patient age was 10.6 years (range, 7–15 years) and the mean modified cyst index was 6.56 (range, 4.95–8.25). The mean cyst healing period was 8.7 months (range, 4–30 months) and the mean follow-up period was 31.05 months (range, 24–42 months). Seventeen lesions (89%) were classified as completely healed and two (11%) were classified as healed with residual radiolucency. In all cases, no angular deformity was found on the final follow-up radiograph. Therefore, preventive flexible intramedullary nail insertion before the occurrence of a pathologic fracture because of simple bone cysts with a modified cyst index of at least 4 in the proximal humerus is an excellent treatment option. Level of Evidence: Therapeutic Level IV.