Purpose: A 56-year-old female with a medical background presented with persistent lower back pain. Initially attributing the pain to muscle strain, the discomfort extended from her buttocks to both legs, predominantly on the left side, over a span of three months. An MRI of her lumbar spine revealed a round hypointense lesion at L5/S1 on T1WI that brightened on T2WI, suggestive of a left-sided spinal canal synovial cyst. Under the provisional diagnosis of a spinal tumor, she was admitted for surgical intervention. Materials and Methods: With informed consent, a surgical intervention was performed, where the left L5/S1 ligamentum flavum was removed, along with the extradural cystic lesion, relieving pressure on the left S1 root. The histology showed a collagenous fibrous wall, devoid of a synovial lining cell, which is compatible with ganglion cyst. Results: Postoperatively, the patient exhibited a significant improvement in her S1 root pain during a one-month follow-up. This case underscores the importance of accurate diagnosis and timely surgical intervention in managing spinal cystic lesions. Conclusion: Synovial and ganglion cysts are typically found around peripheral joints and tendon covers, yet they are infrequently observed within the spine. While these cysts often originate from the facet joint, there have been instances where they are connected to various spinal structures, including the ligamentum flavum and even the disc. As these cysts grow, particularly when linked with degenerative alterations, they can press against the nearby thecal sac or nerve root. We presented a case of ganglion cyst at the lumbosacral spine and discussed clinical, radiological, and surgical findings with good prognosis.