Non-specific low back pain in athletes can be caused by discogenic back pain, Modic type 1 change, and facet joint arthritis. In this report, we describe a full-endoscopic surgical strategy that we have used to treat a patient with both discogenic pain and Modic type 1 change. The patient was a 32-year-old professional baseball player who played an infield position and had a 2-year history of low back pain. Three years earlier, he had undergone micro-endoscopic discectomy for left herniated nucleus pulposus at L5/S1. His leg symptoms resolved postoperatively, and he returned to playing baseball the following season. However, his low back pain gradually increased. Two years after the initial surgery, he was experiencing low back pain in daily life and found it very difficult to play baseball. Short T1 inversion recovery (STIR) magnetic resonance imaging (MRI) revealed Modic type 1 change and high-signal intensity zones in degenerated discs at L4/5 and L5/S1. Injection of xylocaine 1% reduced the pain temporarily, confirming that the pain generator was at L4/5 and L5/S1. The pathological diagnosis was discogenic pain with Modic type 1 change. We performed full-endoscopic disc cleaning (FEDC) surgery for the Modic type 1 change and thermal annuloplasty (TA) for the discogenic pain at these levels. The patient's low back pain decreased steadily thereafter. Six months after surgery, he returned to baseball, playing for a full season without pain. We have successfully treated a professional baseball player with discogenic pain and Modic type 1 change by full-endoscopic surgery.