We report a rare case of an elite para-athlete with lumbar disk herniation whose pain generator was difficult to diagnose and treat. A 28-year-old woman with paraplegia below the T10 level felt pain in her low back and left leg during a match. Magnetic resonance imaging revealed a lateral lumbar disk herniation and a high-intensity zone on the left side at the L5-L6 level. Because the pain disappeared following L5 selective nerve block, we performed transforaminal full-endoscopic discectomy alone. Despite the disappearance of leg pain after surgery, her low back pain persisted. We performed thermal annuloplasty because reproducible pain and subsequent temporary pain relief by discography and discoblock after the initial surgery indicated discogenic pain. Her suffering from back pain gradually reduced. She returned to competition 2 months after the second surgery without intensive rehabilitation due to difficulty in performing core exercises for abdominal muscles. During the return match, she experienced a relapse of pain in the low back and left leg, which was caused by a recurrence of disk herniation. We performed a full-endoscopic discectomy with thermal annuloplasty again. Her clinical symptoms were immediately relieved. We enhanced her thoracic spine flexibility to prevent subsequent recurrence. Finally, she returned to international competition 2 months after the third surgery. Close attention to para-athletes is required to achieve an accurate diagnosis of pain generators and prevent recurrence due to their distinctive disorders. Thermal annuloplasty and rehabilitating thoracic movement can be an excellent option for para-athletes with discogenic low back pain.