The pathogenesis of slippage in pediatric spondylolisthesis is still unclear, although epiphyseal injury may account for many cases based on preclinical studies. However, no reports have described a pediatric case of isthmic spondylolisthesis showing radiologic evidence of epiphyseal injury. We report such evidence in a 13-year-old boy with low-back pain. Radiography revealed rounding of the S1 surface, a fracture line below the S1 endplate surface, and a bone marrow lesion in addition to slippage. Slippage and the rounding deformity were partially reversed (from 20 to 14% and from 42 to 27%, respectively) with conservative treatment and natural bone remodeling.