Aim The aim of this study was to compare the outcome of amniotic membrane transplantation (AMT) and topical mitomycin-C (MMC) in the management of recurrent pterygia. Patients and methods This is a retrospective study that included 40 cases of recurrent pterygia. They were subjected to surgical excision of the pterygium with bare sclera technique. The cases were categorized into two groups, 20 cases in each group. Group 1 was managed with intraoperative topical MMC, while group 2 was managed with AMT at the time of surgery. The patients were followed-up for at least 6 months postoperatively. The outcome measures were visual acuity (VA), corneal astigmatism, recurrence, and postoperative complications. Results The duration of postoperative pain was significantly shorter in the AMT group (6.8±1.0 days) than in the MMC group (10.45±1.5 days, P<0.0001). In addition, postoperative photophobia and lacrimation persisted for a significantly longer period in the MMC group (mean=10.0±1.03 days) compared to the AMT group (mean=7.85±0.81 days, P<0.0001). At the end of follow-up period, VA improvement occurred in 60% of group 1 and in 70% of group 2 patients. However, the preoperative and postoperative decimal VA were not significantly different between the two study groups (P=0.6684 and 0.7302, respectively). In group 1, there was a significant difference between the preoperative corneal astigmatism [−3.74±2.19 diopter (D)] and the postoperative astigmatism (−2.31±1.46 D) after 6 months (P<0.01). Similarly, in group 2, there was also a significant difference between the preoperative corneal astigmatism (−3.83±2.32 D) and the postoperative astigmatism (−2.12±1.60 D) after 6 months (P<0.01). However, the difference between the two groups was statistically insignificant. In the first postoperative 2 weeks, there was a statistically insignificant higher incidence of delayed wound healing and superficial punctate keratitis in the MMC group. The corneal wound healing was faster in the AMT group (mean=4.2±0.69 days) than in the MMC group (mean=4.6±o.6 days). However, the difference was not statistically significant (P=0.0578). At 2 weeks postoperatively, there were two cases of conjunctival defect and one case of scleral thinning in the MMC group only. At the end of the follow-up period, another case, in the MMC group, developed scleral thinning; however, the cornea was clear. Conclusion AMT and MMC could be used in the management of recurrent pterygia. The AMT group showed better visual outcome without postoperative complications. However, the difference between the two groups was statistically insignificant.