BACKGROUND: Percutaneous transforaminal endoscopic lumbar decompression (PTELD) is an emerging surgical alternative for treating lumbar spinal stenosis (LSS). However, the foraminoplasty procedure often requires repeated fluoroscopy, and endoscopy just offers a local view. No studies have focused on decreasing radiation exposure with electromagnetic navigation assistance. This study introduces a novel electromagnetic-based navigation (EMN) endoscopic system for PTELD in patients with LSS and compares the results in navigation and fluoroscopy groups. METHODS: Eighty-eight patients with LSS were randomized into either a navigation (44 patients) or fluoroscopy group. Duration of surgery, cannula placement time, radiation dose, blood loss, intraoperative pain assessment, and postoperative hospitalization stay were evaluated. The clinical outcomes were evaluated using a visual analogue scale (VAS), the Oswestry Disability Index (ODI), 6-minute walk test, and modified Macnab criteria. RESULTS: Eighty-five patients were followed-up for at least 12 months. The duration of surgery and cannula placement time were significantly more efficient in the navigation group (P=0.03 and P<0.001). Intraoperative pain assessment showed significantly less pain in the navigation group (P=0.038). The radiation dose was significantly higher in the fluoroscopy group than the navigation group (P<0.001). The VAS scores for back (P<0.001) and leg (P<0.001) pain improved significantly in both groups after surgery, as did the ODI (P<0.001) scores. Improvements in walking ability and Macnab criteria assessments at the 12-month follow-up, assessed subjective by patient assessments did not differ between the two groups. CONCLUSIONS: The EMN system used in PTELD for patients with LSS compared to fluoroscopy enhances efficiency for foraminoplasty, reduces intraoperative pain and levels of radiation exposure. It results in outcomes comparable with results using fluoroscopy.