Long-term use of cell phones emitting electromagnetic fields (EMFs) have raised concerns regarding public health in recent year. We aimed to investigate the possible effects of 900 MHz EMF exposure (60 min/day for 28 days) on the rat testis. Another objective was to determine whether the deleterious effect of EMF radiation would be reduced by the administration of thymoquinone (TQ) (10 mg/kg/day). Twenty-four male adult Wistar albino rats were randomly selected, then assigned into four groups as followControl, EMF, TQ and EMF + TQ. Testicular samples were analyzed using histological, stereological, biochemical and immunohistochemical techniques. Total numbers of primary spermatocytes and spermatids as well as Leydig cells were significantly decreased in the EMF group compared to the Control group (p < 0.05). In the EMF + TQ group, the total number of primary spermatocytes was significantly increased compared to the EMF group (p < 0.05). Superoxide dismutase (SOD) activity was significantly increased in the EMF group compared to the Control group (p < 0.05). Also, serum testosterone levels and wet weight of testes were significantly decreased in the EMF group compared to the Control group (p < 0.05). Our findings suggested that exposure to a 900 MHz EMF had adverse effects on rat testicular tissue and that the administration of TQ partially mitigated testicular oxidative damages caused by EMF radiation.