Abstract Background Chronic lumbar zygapophysial joint pain is a common cause of chronic low back pain. Percutaneous radiofrequency ablation (RFA) is one of the effective management options; however, the results from the traditional RFA need to be improved in certain cases. The aim of this study is to investigate the effect of percutaneous radiofrequency ablation under endoscopic guidance (ERFA) for chronic low back pain secondary to facet joint arthritis. Methods This is a prospective study enrolled 60 patients. The cases were randomized into two groups: 30 patients in the control group underwent traditional percutaneous radiofrequency ablation, others underwent ERFA. The lumbar visual analog scale (VAS), MacNab score, and postoperative complications were used to evaluate the outcomes. All outcome assessments were performed at postoperative 1 day, 1 month, 3 months, 6 months, and 12 months. Results There was no difference between the two groups in preoperative VAS (P > 0.05). VAS scores, except the postoperative first day, in all other postoperative time points were significantly lower than preoperative values each in both groups (P 0.05). However, the EFRA demonstrated significant benefits at the time points of 3 months and 6 months (P > 0.05). The MacNab scores of 1-year follow-up in the ERFA group were higher than that in the control group (P < 0.05). The incidence of complications in the ERFA group was significantly less than that in the control group (P < 0.05). Conclusions ERFA may achieve more accurate and definite denervation on the nerves, which leads to longer lasting pain relief.