Azoospermia, characterized by the absence of sperm in ejaculation, is a severe male infertility condition resulting from defects in spermatogenesis or the testicular duct system. DNA-alkylating agents, often from chemical drugs, contribute to infertility, while antioxidants play a crucial role in addressing fertility issues in couples facing subfertility. Traditional medicinal plants, particularly saffron, have been recognized for their fertility-enhancing effects. Crocins in saffron are noted for their potential to improve fertility indicators in rat models. This study aimed to investigate the effects of the combination of letrozole and crocin on sperm motility and biochemical markers in azoospermia, complemented by gene expression analysis. Thirty male Wistar rats were divided into five groups: control, azoospermia, azoospermia with letrozole, azoospermia with crocin, and azoospermia with both letrozole and crocin. Azoospermia was induced using a 10 mg intraperitoneal injection of busulfan over ten days. Subsequent analyses included histopathological, molecular, and hormonal assessments, with data analyzed using Graph Prism software. The combination treatment with letrozole and crocin significantly improved sperm motility compared to the azoospermia group, while reducing motility compared to the control group. Additionally, there was an increase in total sperm count, Total Antioxidant Capacity (TAC), and testosterone levels, accompanied by a decrease in Total Oxidant Status (TOS) enzyme activity (P < 0.05). QRT-PCR analysis indicated decreased expression of the GDNF gene compared to the control (P < 0.001) but increased expression compared to the azoospermia group (P < 0.001). Likewise, 5-alpha-reductase gene expression showed a significant decrease (P < 0.05). Therefore, the synergistic administration of crocin and letrozole holds promise for mitigating DNA damage caused by busulfan, potentially reducing long-term damage to bone marrow and improving fertility outcomes.