Lumbar disc prolapse (LDP) is a significant cause of low back pain and radiculopathy. While both Microlumbar Discectomy (MLD) and Microendoscopic Discectomy (MED) are established minimally invasive treatments, comparative data for double-level LDP is limited. This study aimed to compare the efficacy and safety of MED versus MLD for patients with double-level lumbar disc prolapse. This randomized controlled trial included 50 patients with double-level LDP who failed 8 weeks of conservative treatment, randomized equally into two groups: MED group (n = 25) who underwent tubular microendoscopic interlaminar discectomy and MLD group (n = 25) who underwent standard microlumbar discectomy. Patients were followed for one year postoperatively. Primary outcomes included Visual Analogue Scale (VAS) scores for back and leg pain. Secondary outcomes encompassed Oswestry Disability Index (ODI), operative time, blood loss, wound length, hospital stay, return to work, and postoperative complications. Both MED and MLD significantly improved pain and disability. The MED group demonstrated statistically lower VAS scores for back pain at one month (2.1 ± 0.73 vs. 2.7 ± 0.84, p = 0.012), and consistently lower VAS scores for both back and leg pain at 6 and 12 months postoperatively. Operative time was significantly longer for MED (103 ± 15.6 mins vs. 73 ± 14.9 mins, p < 0.001). However, MED was associated with significantly less blood loss (49.9 ± 10.1 mL vs. 87.2 ± 26.2 mL, p < 0.001), smaller wound length (2.3 ± 0.4 cm vs. 4.7 ± 0.5 cm, p < 0.001), shorter hospital stay (1.1 ± 0.61 days vs. 1.7 ± 0.58 days, p = 0.007), and earlier return to work (39.4 ± 7.24 days vs. 43.1 ± 3.6 days, p = 0.029). Both microendoscopic and microlumbar discectomy are effective and safe for double-level lumbar disc prolapse. Microendoscopic discectomy offers superior short-term pain relief, reduced invasiveness, shorter hospital stays, and earlier returns to work, despite a longer operative time. These benefits suggest MED as a favorable option for patients with double-level LDP