Cyclophosphamide (CYP) is an effective anti‐cancer drug that is widely accepted, but it is not devoid of unintended toxic effects. Gonadal toxicity is reported as one of the side effects of its long‐time use. This study examined the effects of thymoquinone (TQ) on the biological integrities of the testes after cyclophosphamide exposure. Thirty adolescent male Wistar rats (100–110 g) were divided into six groups (n = 5), receiving normal saline (NS), 20 mg/kg of CYP (CYP), 5 mg/kg of TQ (TQ5), 10 mg/kg of TQ (TQ10), 20 mg/kg of CYP and 5 mg/kg of TQ (CTQ5), and 20 mg/kg of CYP and 10 mg/kg of TQ (CTQ10) respectively. On the 22nd day, blood, semen and testicular samples were collected for the assay of serum reproductive hormones (follicle‐stimulating (FSH) and luteinizing (LH) hormones), semen analysis and testicular histology and proliferating cell nuclear antigen (PCNA) expression. The results revealed that CYP exposure affected functional and structural integrities of the testes, by depleting sperm count and motility, testosterone, LH, spermatogenic and mature sperm cell population, Leydig cells and PCNA immunoreactive proliferating cells. TQ interventions were able to reverse all cytotoxic CYP impacts, but with differential activities on the hormonal concentrations, specifically LH and FSH. Cumulatively, thymoquinone may be a potent agent against cyclophosphamide effects on the physiological, regeneration and histological integrities of the testes, as observed in this study.