Psychotropic stimulants like methamphetamine (METH) have an impact on the physiology, behavior, and psychology of human beings and can damage the reproductive and neuroendocrine systems in them. These deleterious impacts include a temporary drop in the relative weight of the testis along with adverse effects on spermatogenesis. Sambucus nigra, also known as elderberry (EB) or sweet elder, is a source of bioactive compounds that has drawn growing attention for its potential beneficial impact in preventing and treating several diseases. In this experimental research, 36 adult male rats were classified into three groups: (1) control, (2) METH, and (3) METH receiving the EB diet. The rats were injected with METH at a dose of 20 mg/kg for 28 days during treatment with the EB diet. Then, the rats were euthanized, and their sperm samples were collected for sperm parameters analysis. Afterward, the testis samples were taken for histopathological experimentations, immunohistochemistry against TNF-α and caspase-3, and serum testosterone levels. Our findings indicated largely improved sperm and stereological parameters, like spermatogonia, primary spermatocyte, round spermatid, and Leydig cells, and an increased serum testosterone level in the METH group receiving the EB diet compared to the other METH group. The results also revealed a significantly decreased TNF-α and caspase-3 expression in the METH+EB group compared to the METH group. In conclusion, the EB diet is regarded as an alternative treatment for improving the spermatogenesis process in reproductive toxicity induced by METH exposure.