Butterfly vertebra anomaly is a rare condition where the vertebral body fails to fuse during embryogenesis. In this case report, we present a 32-year-old male with progressive lower back pain and paralysis in both lower extremities. CT- and MR-scan showed an isolated L3 butterfly vertebra with a fusion of L2 and L3 discus through the defect and a discus prolapse compressing the spinal canal. The patient underwent successful decompressive surgery and experienced relief in symptoms post-operatively.