Goji berries (), rich in antioxidant and immunomodulatory compounds, have shown potential benefits for male reproductive health. This study aimed to evaluate the impact of dietary Goji berry (GB) supplementation on immune-related and antioxidant gene expression in the male reproductive tract of rabbits. Eighteen 7-month-old New Zealand White rabbit bucks were randomly assigned to two groups: a control group ( = 9) receiving a standard diet, and a Goji group ( = 9) receiving the same diet supplemented with 1% GB. After 60 days of nutritional adaptation and then 60 days of treatment, tissues from the testes, epididymis, seminal vesicles, prostate, and bulbourethral glands were collected and analyzed using quantitative real-time PCR. Gene expression analysis focused on immune markers (TLR4, IL-1β, IL-10, and TNFα) and antioxidant enzymes (SOD1, CAT, and GPX). Significant modulation was observed only in the epididymis, where TLR4 and GPX were significantly downregulated in the Goji group ( = 0.0274 and = 0.007, respectively), while IL-1β and TNFα showed a downward trend. No significant differences were found in the other tissues. These results suggest that Goji berry supplementation exerts tissue-specific effects, particularly in the epididymis, by modulating inflammation and oxidative stress. This supports its potential use as a natural nutraceutical strategy to enhance male fertility in rabbits.