One of the major challenges in modern medicine is the effective treatment of both infected and aseptic wounds. A promising approach involves the use of enzymatic compositions based on proteases, which are capable of selective wound debridement and modulation of the regeneration process. Our study aimed to investigate the dynamics of major growth factors, namely platelet-derived growth factor A (PDGF-A), insulin-like growth factor (IGF), fibroblast growth factor (FGF), epidermal growth factor (EGF), hypoxia-inducible factor-1α (HIF-1α), transforming growth factor-β (TGF-β), vascular endothelial growth factor (VEGF), and nerve growth factor (NGF), in blood serum and skin homogenates of rats with experimentally induced purulent-necrotic wounds under conditions of local application of an enzymatic composition. The experiment was performed on 50 adult male outbred white rats, which were evenly divided into two groups: control and experimental. After the induction of a purulent-necrotic skin injury, animals in the experimental group received local treatment with a composition based on proteases isolated from the sea urchin Sterechinus neumayeri and the starfish Odontaster validus, whereas animals in the control group did not receive treatment. Rats were euthanized on days 3, 6, 9, and 14, as well as at the point of complete epithelialization (n = 5). In the serum of control animals, a maximal increase in the levels of the investigated growth factors was observed as early as day 3, which was likely the result of an excessive inflammatory response and uncoordinated hypersecretion triggered by tissue injury. In contrast, in the serum of experimental animals, elevations in growth factor levels were detected not immediately, but during the phase of active proliferation (days 6-14), suggesting a physiologically mediated activation of reparative processes. At the same time, in skin homogenates, only a moderate increase in the concentrations of growth factors was recorded compared to controls, which may indicate a reduction of the local inflammatory burden and a more balanced regenerative response. Thus, we propose that local application of a protease-based composition derived from marine hydrobionts contributes to the modulation of key growth factor levels, attenuates excessive local responses, and improves the quality of tissue repair.