The aim of the present study was to compare the effects of folinic acid chitosan hydrogel and botulinum toxin A on the wound repair of cleft lip surgery in rat animal models. Cleft lip defects were simulated by triangular incisions in the upper lip of 40 Wistar rats. Then, the rats were randomly assigned to four groups: control (CTRL), chitosan hydrogel (CHIT), and folinic acid chitosan hydrogel (FOLCHIT), in which the wounds were covered by a gauze pad soaked in normal saline, chitosan hydrogel, and folinic acid chitosan hydrogel, respectively for 5 min immediately after closure; and botulinum toxin A (BOT) with the injection of 3 units of botulinum toxin A in the wound region. Fibroblast proliferation, collagen deposition, inflammatory cell infiltration, neovascularization, and epithelial proliferation and each parameter were rated on days 14 and 28. Statistical analysis was performed by Kolmogorov-Smirnov test, Shapiro-Wilk test, Kruskal-Wallis, and post-hoc tests (α = 0.05). The mean score for fibroblast proliferation was significantly higher in the FOLCHIT group compared with the BOT group at days 14 and 28 (p < 0.001, p = 0.012, respectively). At day 28, collagen deposition was significantly higher in the FOLCHIT group compared with the BOT group (p = 0.012). No significant difference was observed between the inflammatory infiltration of the study groups at the two time points (p = 0.096 and p = 1.000, respectively). At day 14, vascular proliferation of group FOLCHIT was significantly higher than groups CTRL and CHIT (p = 0.001 and p = 0.006, respectively). The epithelial proliferation in the FOLCHIT group was significantly higher than groups CHIT and CTRL at day 14 (p = 0.006 and p = 0.001, respectively) and day 28 (p = 0.012). In simulated lip cleft defects, topical application of folinic acid induces faster initial regeneration by higher inflammation and cellular proliferation, at the expense of a higher tendency for scar formation by slightly higher fibroblast proliferation and collagen deposition. While injection of botulinum toxin A provides less fibroblast proliferation and collagen deposition, and thus lower potential for scar formation compared with the folinic acid group. Therefore, in wounds of the esthetic zone, such as cleft lip defects, the application of botulinum toxin A shows promising results.