This study was conducted to define whether pigment epithelial-derived growth factor (PEDF), together with docosahexaenoic acid (DHA), enhances the synthesis of neuroprotectin D1 (NPD1) and the regeneration of corneal nerves damaged after surgery. Corneal stromal dissection was performed in the left eyes of adult New Zealand rabbits treated with DHA+PEDF, PEDF, or DHA for 6 weeks. In vivo confocal images of the corneas were obtained at 2, 4, and 8 weeks, and nerve areas were quantified. At 8 weeks after treatment, corneas were stained with tubulin betaIII antibody, and the epithelial nerve area and the sub-basal and stromal nerve plexus were quantified. At 1 week and 2 weeks after treatment, lipids were extracted from corneas, and the synthesis of NPD1 was analyzed by mass spectrometry. Epithelial cell density was quantified by confocal microscopy 8 weeks after surgery. In vivo confocal images at 2 and 4 weeks after surgery showed a 2.5-fold increase in corneal nerve area in PEDF+DHA-treated animals compared with control animals. Increased nerve surface areas in epithelia, subepithelia, and stroma were observed in rabbits treated for 8 weeks with PEDF+DHA. PEDF or DHA alone did not produce a significant increase. NPD1 synthesis peaked at 1 week and was four times higher in the PEDF+DHA-treated group than in the controls. PEDF+DHA promotes the regeneration of corneal nerves. Neurotrophin-mediated NPD1 synthesis is suggested to precede nerve regeneration by demonstration of its accumulation upon addition of DHA and PEDF at earlier time points. Therefore, this signaling mechanism upregulates corneal nerve regeneration and may be targeted in neurotrophic keratitis, dry eye after refractive surgery, and other corneal diseases.