Bertolotti’s syndrome is a syndrome in which the transverse process of the most caudal lumbar vertebra becomes enlarged and articulates with the sacral alar, causing back pain. Here, we report a case of an adolescent basketball player with Bertolotti’s syndrome who was unable to resume playing despite conservative treatment and underwent an endoscopic partial transverse process and sacral alar resection. A 16-year-old male basketball player presented to our hospital with a chief complaint of left low back pain during exercise and prolonged sitting for over one month. No obvious neurological abnormality was found. X-rays and CT showed lumbosacral transitional vertebrae, and the left transverse process of the sixth lumbar vertebra articulated with the sacrum and iliac, which was the Castellvi classification IIA. A block injection into the articulated surface produced improvement in pain, but the effect was not sustained. Since the patient was refractory to conservative treatments, such as medication and physiotherapy, surgery was performed. During surgery, the articulated transverse process and sacral alar were partially resected endoscopically. Because of the proximity of the resection site to the S1 nerve root, intraoperative electromyography (free-run EMG) was used to detect nerve root irritation symptoms in real time. The patient had no postoperative complications, his low back pain improved immediately, and he returned to play basketball three months after surgery. One year after surgery, the bone resection site showed gradual bone regeneration, and two years after surgery, the transverse process and sacral alar showed a bony bridge. The transverse process was enlarged compared to immediately after surgery but remained smaller than that before surgery. The patient continued to play basketball for two years after surgery without back pain, and no symptoms due to bone regeneration appeared. In the present case, a partial resection of the transverse process and sacral alar was performed with good results. Because the bone resection site was close to the S1 nerve root, the use of an endoscope and intraoperative free-run EMG allowed for a safer procedure during the bone resection. In addition, the patient did not present with symptoms that would affect his basketball performance, although the bone regenerated and bridging occurred between the transverse process and sacral alar over a two-year postoperative course.