Dorsal ramus medial branch radiofrequency ablation is reported to be effective for refractory lumbar facet joint syndrome. However, as nerve fibers can regenerate, the therapeutic effect was reported to be short and last only 6 to 12 months. Previously, we reported a novel endoscopic joint capsule and articular process excision procedure. In that case, a satisfying effect was achieved by removing the culprit hyperplastic articular synovial entrapped in the joint space endoscopically. We presume this treatment is an etiologic treatment and can exert longer-term efficacy. This retrospective clinical trial aimed to elucidate the longer-term efficacy as well as the safety profile of the procedure. This was a retrospective descriptive study. The participants underwent endoscopic joint capsule and articular process excision procedures. The Oswestry Disability Index (ODI) and Visual Analogue Scale (VAS) before the operation, and at 3 months, 6 months, 1 year, and 2 years post-operation were recorded by reviewing medical charts and conducting telephone interviews. A total of 234 participants were evaluated in the trial. After participant screening, 13 participants were included in the final analysis. The VAS score was reduced from (median (P25, P75)) 6 (4.5, 6) at pre-operation to 2 (0, 4) at 1-year post-operation and 0 (0, 1) at 2-year pre-operation. The ODI score was reduced from 37.78 (27.09, 59.95) at pre-operation to 8.89 (2.22, 24.34) at 1-year post-operation and 6 (0.02, 11.11) at 2-year post-operation. The difference was statistically significant. Further subgroup analysis demonstrated that a narrowed intervertebral space was a possible relevant factor for poor outcomes. No procedure-related complications were reported. Endoscopic joint capsule and articular process excision is an effective and safe procedure for refractory lumbar facet joint syndrome. The effectiveness duration can last up to 1 to 2 years.