We evaluated how well 0.1% RGN-259 eye drops (formulated with the regenerative peptide thymosin ß4) support the resolution of persistent epithelial lesions in individuals diagnosed with Stage 2 or Stage 3 neurotrophic keratopathy. After 4 weeks, full closure of defects was documented in 6 of the 10 participants treated with RGN-259, compared with 1 of the 8 in the placebo arm (p = 0.0656), suggesting a strong therapeutic signal. Additional evidence of benefit was reflected in the significant healing rate (p = 0.0359), with no defect recurrence noted at day 43—two weeks post-treatment—while the sole placebo responder at day 28 showed relapse at day 43. Improvements in the Mackie stage were recorded at Days 29, 36, and 43 for the RGN-259 cohort (p = 0.0818, 0.0625, and 0.0467). Time-to-healing also favored RGN-259 (p = 0.0829, Kaplan–Meier). Participants receiving RGN-259 reported a significant reduction in ocular discomfort, foreign-body sensation, and dryness at various assessment points, unlike those given placebo. No meaningful safety concerns emerged. Overall, 0.1% RGN-259 accelerated epithelial recovery in neurotrophic keratopathy, enhanced comfort, and demonstrated a favorable safety profile.