The imaging findings in some cases of low back pain are difficult to describe and the pathophysiology is not clear because subjective findings are usually difficult to document. This report concerns a rare case about the lumbosacral joint causing persistent severe back pain which in itself does not usually have any pathological meaning. We describe the diagnosis, treatment, and outcome of a patient suffering from low back pain with lumbosacral transitional vertebra. The radiological examination showed the congenitally malformed transverse processes of the 5th lumbar vertebra to create a facet joint-like shape at the sacral ala region on both sides. Surgery resulted in immediate disappearance of the low back pain. When the lumbosacral junction shows some instability without fusion, the joint-like region could be the cause of low back pain. The lumbosacral transitional vertebra may be associated with low back pain. Electric denervation of the space between the transverse process of 5th lumbar vertebra and sacral ala is minimally invasive and effective for pain eradication.