The aim of the present study was to report a new technique for electromagnetic navigation system-assisted percutaneous full-endoscopic foraminoplasty and discectomy and to evaluate the efficacy of this technology in the treatment of lumbar disc herniation (LDH). This is a retrospective study. Seventeen patients who underwent electromagnetic navigation system-assisted percutaneous full-endoscopic foraminoplasty and discectomy in our department from September to November 2018 were included in the study. Patients' hospital charts, magnetic resonance imaging results, surgical data and follow-up records were reviewed. Outcomes were assessed by visual analog scale (VAS) score, Oswestry Disability Index (ODI), modified MacNab criteria and postoperative complications. The median follow-up time was 20.64 months (range, 19-21 months). The average operating time was 52.94±12.88 min (range, 35-78 min), including the working tube introduction time (13.59±2.89 min), decompression time (39.35±13.61 min), and the fluoroscopic time (3.65±2.52 min). Postoperative back VAS, leg VAS, and ODI were significantly improved compared with pre-operation, respectively (P<0.01). The overall excellent and good rate of these seventeen patients was 94%. There were no significant complications related to the operation. Electromagnetic navigation system-assisted percutaneous full-endoscopic foraminoplasty and discectomy is a safe and effective method for treating LDH and this method has the advantage of short operative time and fluoroscopic times.