Background: Morphine is a pain medication of the opiate type and one of the major risk factors for disorders of the body organs and causes disturbing effects. Thymoquinone is a phytochemical compound found in the plant Nigella sativa. It has different pharmacological effects such as anticancer and antioxidant. Objective: This study was designed to evaluate effects of thymoquinone against morphine damages on pancreas of mice. Material methods: In this study, forty-eight male mice were divided into six groups (n=8). Saline group (control), morphine group (20 mg/kg) and groups receiving thymoquinone (4.5, 9 and 18 mg/kg) and morphine plus thymoquinone (4.5, 9 and 18 mg/kg) intraperitoneally for 3 days. The diameter and number of the islets of Langerhans, the pancreas weight and serum levels of nitric oxide, glucose and insulin levels have been studied. Result: The results indicated that morphine administration significantly decreased pancreas weight, diameter and number of the islets and serum levels of insulin and nitric oxide and increased glucose levels to saline group (P<0.05). However, thymoquinone and thymoquinone plus morphine administration significantly boosted pancreas weight, diameter and number of the islets and serum levels of insulin and nitric oxide and reduced glucose levels in all doses compared to morphine group (P<0.05). Conclusion: It seems that thymoquinone can improve pancreas injuries induced by morphine in mice.