Purpose: To evaluate the clinical efficacy of amniotic membrane extract eye drops (AMEEDs) in patients with persistent epithelial defects (PEDs) of the cornea.Methods: Sixteen patients with PEDs refractory to the conventional treatment were further treated with AMEEDs six times a day. Visual acuity, visual analog scale (VAS), esthesiometer score, and areas of the epithelial defects before and after 1 and 2 months of treatment were evaluated. After 2 months, AMEEDs were considered effective if all epithelial defects were healed, partially effective if the epithelial defects decreased in size compared with the baseline, and ineffective if the epithelial defects increased in size and required additional treatment.Results: After 2 months of treatment with AMEEDs, there was a reduction in the area of epithelial defects (5.2 ± 3.1 mm2 vs. 0.1 ± 0.1 mm2, respectively, p = 0.01), as well as a significant improvement in best-corrected visual acuity (0.8 ± 0.5 logarithm of minimal angle of resolution [LogMAR] vs. 0.6 ± 0.3 LogMAR, respectively, p = 0.03), and VAS scores (4.3 ± 1.0 vs. 2.8 ± 0.7, respectively, p = 0.04) compared with the baseline values. Treatment with AMEEDs was effective in 13 (81.3%) patients and partially effective in three (18.8%) patients.Conclusions: AMEEDs could stimulate epithelial wound healing and improve ocular symptoms in patients with refractory PED. Therefore, AMEEDs could be considered an effective treatment option for refractory PEDs.