Exposure to electromagnetic field in long-term use of cell phones has increased concerns about serious health problems. Our aim was to survey the possible effects of electromagnetic field radiation (60 min/day for 28 days) on the spinal cords of 12 weeks old rats. Further, we investigated whether the administration of thymoquinone (10 mg/kg/day) would protect the spinal cord tissue against the adverse effects of electromagnetic field or not. Twenty-four adult male Wistar albino rats were assigned randomly into four groups: control, electromagnetic field, thymoquinone and electromagnetic field + thymoquinone. The cervical spinal cords of all rats was evaluated using the stereological, biochemical and histological methods. The number of motor neurons were reduced in the electromagnetic field group compared to the control group (p < 0.05). Superoxide dismutase level was higher in the electromagnetic field group compared to the control group (p < 0.05). In the electromagnetic field + thymoquinone group, we found an increase in the number of motor neurons and decrease in superoxide dismutase activity compared to the electromagnetic field group (p < 0.05). Our histological findings also exhibit the remarkable architectural alterations. We speculated that electromagnetic field radiation induced the morphological and biochemical damage to the spinal cord tissue of rats. Administration of antioxidant, thymoquinone, also ameliorated such complications caused by electromagnetic field.