Objective Facet joint cysts (FJCs) of the lumbar spine are an increasingly reported cause of radiculopathy, lower back pain, and neurologic deficits. Currently, there is a lack of conclusive evidence outlining when a particular treatment should be undertaken and what patient indications suit a particular approach. The present systematic review and meta-analysis aims to evaluate the efficacy of percutaneous treatment and surgical decompression with or without fusion. Methods A systematic literature search of scientific databases from their inception to February 2016 was performed by 2 reviewers. Studies pertaining to percutaneous procedures, decompressive surgeries, or decompressive surgeries with fusion for the treatment of lumbar facet joint cysts were identified. Data for resolution of symptoms, repeat procedures, and subsequent fusion were extracted and analyzed. Results Fifty studies comprising 870 patients with lumbar FJCs were identified for inclusion. Decompressive procedures were performed in 62.8% of patients, whereas 36.1% were treated by percutaneous aspiration or rupture, and only 1.1% were treated by decompression with fusion. Pooled analysis showed the rate of cyst resolution to be 90% for decompressive procedures with or without fusion and 58% for percutaneous procedures. Repeat procedures were required in 29% of percutaneous procedures, but less than 1% for all decompression operations. Conclusions Evaluation of the literature shows surgical intervention to be advantageous over percutaneous procedures for the treatment of lumbar FJCs. There is no evidence suggesting when fusion should be undertaken because of the limited data available.