Percutaneous endoscopic lumbar decompression (PELD) shows promise for lumbar spinal stenosis (LSS) treatment, but its use is limited by the disease's complexity and procedural challenges. In this study, the effects of preoperative planning and intraoperative guidance with computed tomography (CT)/magnetic resonance imaging (MRI) registration techniques on PELD for LSS and postoperative rehabilitation outcomes were evaluated. This retrospective study was conducted with data from patients who underwent PELD for LSS between January 2021 and December 2023. Patients were assigned to preoperative CT/MRI registration and control groups. Data collected included the operative time, length of hospital stay, visual analog scale (VAS) scores for low back and leg pain, and the Japanese Orthopaedic Association (JOA) lumbar spine score. Differences between groups were assessed using Student's t test. Data from 135 patients (71 in the CT/MRI registration group, 64 in the control group) were analyzed. The operative time was significantly shorter in the CT/MRI registration group (P = 0.007). At 2 months postoperatively, both groups showed significant reductions in VAS leg and low back pain scores (all P < 0.001) and improvements in the JOA score (both P < 0.001). No complication or death occurred. Preoperatively, pain and JOA scores were similar between groups (P = 0.830, P = 0.470, and P = 0.287, respectively). At 2 months postoperatively, patients in the CT/MRI registration group reported lower leg and low back pain levels (P < 0.001 and P = 0.001, respectively) and had higher JOA scores (P = 0.004) than did patients in the control group. Preoperative CT/MRI registration for PELD for LSS reduced the operative time and VAS pain scores at 2 months and improved JOA scores, demonstrating enhanced effectiveness and safety.