Mitomycin C (MMC) and 5-fluorouracil (5-FU) are the most frequently utilized adjuvant therapies in trabeculectomy (TRAB), but there is no general consensus as to the direct comparative efficacy and safety of these two adjuvants. In this study, the authors conducted a meta-analysis to compare the efficacy and safety of augmenting TRAB with MMC or 5-FU. A systematic review with meta-analysis was conducted and five randomized controlled clinical trials comparing MMC versus 5-FU as adjunctive therapies were identified, totaling 416 participants. A lower pooled mean IOP and higher complete and qualified success rates were observed in the MMC arm than in the 5-FU arm. Epithelial corneal defects were the unique complication reported more frequently with 5-FU compared to MMC treatment. Compared to TRAB with 5-FU, TRAB with MMC was associated with higher rates of complete and qualified surgical success and was not associated with increased incidences of postoperative complications.