Background: Percutaneous transforaminal endoscopic discectomy (PTED) and microendoscopic discectomy (MED) are alternative minimally invasive procedures for the treatment of symptomatic lumbar disc herniation (LDH). However, insufficient literature exists to highlight the differences between the procedures. Objectives: This study intended to clarify whether PTED results in better clinical outcomes compared with MED in the surgical management of single-level LDH. Study Design: A multicenter retrospective cohort study. Setting: This study took place in 2 spinal minimally invasive centers in Beijing, China. Methods: A multicenter retrospective study was conducted in consecutive patients diagnosed with symptomatic LDH receiving PTED or MED in 2 spinal minimally invasive centers from April 2009 to July 2016. A total of 1,053 patients were recruited, of which 632 underwent PTED and 421 underwent MED. All patients were followed with a minimum of 2 years; a set of clinical outcomes were extracted and analyzed. Results: The operation time was similar between groups (71.2 +/- 15.1 minutes in the PTED group and 69.4 +/- 12.5 minutes in the MED group; P = 0.518); length of incision was significantly shorter; intraoperative blood loss was less in the PTED group (P < 0.001); hospital stay was 3.6 +/- 1.5 days in the PTED group and 5.4 +/- 2.8 days in the MED group with significant differences detected (P = 0.018); however, intraoperative fluoroscopy was longer with significantly higher cost with the PTED group (P < 0.001). Transient dysesthesia and wound complications were more common in the MED group (P = 0.039 and P = 0.026, respectively); however, no significant differences were found with total complications (P = 0.139). Significant lower Visual Analog Scale pain score (back and leg) were detected on day 1 postoperatively (P = 0.007 and P = 0.018, respectively). No significant differences were found at all other time points (P > 0.05). Significantly better Oswestry Disability Index (ODI) score was detected postoperatively at 1 month in the PTED group (19.6 +/- 9.8 vs. 27.2 +/- 9.3; P = 0.016); ODI score at other time points did not differ significantly between groups (P > 0.05). Modified MacNab criteria showed that most patients experienced excellent and good results with no significant differences between groups (P = 0.511). Limitation: This was a multicenter retrospective study wherein the surgeons may have introduced bias to the study. Conclusions: Both PTED and MED present to be an acceptable long-term efficacy for the treatment of LDH. Although PTED is associated with longer intraoperative fluoroscopy and a little more cost, it should still be considered superior to MED considering the benefits of lesser invasion, shorter hospital stays, quicker pain relief, and functional recovery.