We evaluate the biological and physicochemical effects of a Fusarium oxysporum crude extract (CE) on the skin of healthy rats. The CE is topically applied and subsequently the skin is collected after 3, 6, 12, and 24 h. The samples are analyzed by Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) and histomorphometric analysis. Terminal dUTP nick end labeling (TUNEL assay) is performed to detect both the cells in apoptosis and proliferation. There is a thickening of the epidermis after 6, 12, and 24 h and dermis after 12 and 24 h of CE application. A reduction of the dermis thickness is observed at 3 and 6 h. The treated skin shows higher labeling intensity by TUNEL at 3 h, while a higher intensity by proliferating cell nuclear antigen occurs at 3 and 12 h. FTIR-PAS data support the histology observations showing an increase in the absorption peaks in the dermis after the application of the CE. F. oxysporum CE permeated through the epidermis and the dermis, reaching the subcutaneous tissue, inducing cell apoptosis, and causing physicochemical changes in the organic molecules located in the dermis. This is the first known study associating histopathological and physical chemistry changes on healthy skin after the application of F. oxysporum CE.