Background Electromagnetic navigation-guided technique is an exciting innovative procedure, which has been applied in neurosurgery, otolaryngology, oral and maxillofacial surgery, etc. However, no previous study of the application of electromagnetic navigation to guide endoscopic surgery of disc herniation has been reported. Here, we introduce a new technique of electromagnetic navigation system assisted percutaneous full-endoscopic lumbar foraminoplasty and discectomy and compare it to conventional TESSYS technique. Methods This is a prospective, randomized controlled trial. The observation group was treated with SEESSYS, and the control group was treated with the traditional Transforaminal Endoscopic Spinal Surgery System (TESSYS). Overall surgical time and fluoroscopy time were recorded in all cases. Outcomes of symptoms were evaluated by Visual Analog Scale (VAS) score, Oswestry Disability Index (ODI), and modified MacNab criteria (excellent, good, fair and poor). Results 34 patients (SEESSYS, 17 patients; TESSYS, 17 patients) were enrolled in this study. Both overall surgical time and working tube introduction time were significantly shorter in SEESSYS group than that in TESSYS group (P<0.01). The fluoroscopy time in SEESSYS group was significantly less than that in TESSYS group (P<0.01). Back VAS, leg VAS and ODI at each time point after surgery were not significantly different between two groups (P > 0.05). In both the SEESSYS and TESSYS group, there was a significant decrease in back VAS, leg VAS and ODI at each time point after surgery compared with pre-operation respectively (P<0.01). The excellent and good rate of SEESSYS group was 95%, which is similar to the 90% in TESSYS group. Conclusions Electromagnetic navigation system assisted percutaneous full-endoscopic foraminoplasty and discectomy may be a safe and effective method for treating lumbar disc herniation and this method has the advantages of shortening operative time and fluoroscopy time compared with conventional TESSYS technique. Trial registration The study was registered at Chinese Clinical Trail Registry on Feb 06, 2020 with the registration number: ChiCTR2000029604. (http://www.chictr.org.cn/showproj.aspx?proj=49149)