The aim of this study was designed to evaluate the possible protective effects of thymoquinone (TQ) on the lung injury in rats after chronic toluene exposure. The rats were randomly allotted into one of three experimental groups: control, toluene-treated and toluene-treated with TQ; each group contain 10 animals. Control group received 1 mL serum physiologic and toluene treatment was performed by inhalation of 3000 parts per million (ppm) toluene, in an 8-hr/day and 6 day/week order for 12 weeks. The rats in TQ treated group was given TQ (50 mg/kg body weight) once a day orally for 12 weeks starting just after toluene exposure. Tissue samples were obtained for histopathological investigation. To date, no histopathological changes of lung in rats after chronic toluene exposure by TQ treatment have been reported. Our study showed that TQ treatment inhibits the inflammatory pulmonary responses reducing significantly peribronchial inflammatory cell infiltration, alveolar septal infiltration, alveolar edema, alveolar exudate, interstitial fibrosis and necrosis formation in toluene-treated rats. Our data indicate a significant reduction in the activity of in situ identification of apoptosis using terminal dUTP nick end-labeling (TUNEL), inducible nitric oxide synthase (iNOS) and a rise in the expression of surfactant protein D in lung tissue of toluene-treated with TQ therapy. We believe that further preclinical research into the utility of TQ may indicate its usefulness as a potential treatment on lung injury after chronic toluene exposure in rats.