Background: Microendoscopic discectomy (MED) and percutaneous transforaminal endoscopic discectomy (PTED), as two alternative surgical techniques in minimally invasive spine surgery (MISS), are widely conducted in the treatment of upper lumbar disc herniation (ULDH). This study will systematically assess and compare the clinical outcomes of MED and PTED in treating ULDH combining with the meta-analysis. Methods: All the randomized controlled trials (RCTs) will be searched at the databases including PubMed, EMBASE, Cochrane Library and Web of Science, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), Chinese Scientific Journal Database (VIP), and WANFANG Database from inception to December 2025. The primary outcome will involve Japanese Orthopedic Association (JOA), Oswestry disability index (ODI), and visual analog scale (VAS) scores. The secondary outcomes will be the short-form 36-item (SF-36) health survey questionnaire and the modified MacNab criterion. We will perform data synthesis, subgroup analysis, sensitivity analysis, meta-regression analysis, and the assessment of reporting bias using RevMan 5.3 software. Results: This systematic review will comprehensively evaluate the clinical outcomes of comparison of MED and PTED in the treatment of ULDH and provide a reliable and high-quality evidence. Conclusion: The conclusion of this study will elucidate the clinical outcomes of MED compared with PTED and clarify whether PTED generates better clinical effects than MED in treating ULDH. PROSPERO registration number: CRD 42021244204