Objective: We aimed in this study to investigate the harmful effects of formaldehyde (FA) inhalation and possible protective effects of Nigella sativa (NS) on rats' trachea. Materials and Methods: In this study, 63 adult male rats were used. Animals were divided into nine groups. Group I was used as control group. All other groups were exposed to FA inhalation. Group III, V, VII, and IX were administered NS by gavage. Tissues were examined histologically, and immunohistochemical examination for Bax and caspase-3 immunoreactivity was carried out. Results: Our study demonstrated that FA caused apoptosis in the tracheal epithelial cells. The most apoptotic activity occurred at a 10 ppm dose in a 13-week exposure. Distortion of tracheal epithelium and cilia loss on epithelial surface was present in all groups. However, NS treated Groups VII and IX had decreased apoptotic activity and lymphoid infiltration and protected the epithelial structure, despite some shedded areas. Difference of tracheal epithelial thickness and histological score was statistically significant between Group VI-VII and VIII-IX. Conclusion: FA induces apoptosis and tracheal epithelial damage in rats, and chronic administration of NS can be used to prevent FA-induced apoptosis and epithelial damage.