Late-onset hypogonadism (LOH) is a condition associated with age-related declines in testosterone levels, leading to reduced libido, infertility, muscle deterioration, and cognitive decline in middle-aged men. While testosterone replacement therapy (TRT) is widely used to manage LOH, concerns about its potential side effects highlight the need for safer alternative treatments. Our previous research demonstrated that fermented Morinda citrifolia extract (FME) effectively alleviated LOH-related symptoms in in vitro studies. The present study aimed to investigate the in vivo efficacy of FME in mitigating LOH symptoms using an aged rat model. Male Sprague-Dawley rats (33 weeks old) were administered either Testofen or FME for a duration of four weeks. To evaluate testosterone metabolism and reproductive function, we measured serum testosterone, sex hormone-binding globulin (SHBG), and dihydrotestosterone (DHT) levels, along with testicular gene expression and protein localization. Additionally, physical performance (assessed via treadmill tests), and sperm quality were analyzed. Results showed that FME significantly increased serum testosterone levels while decreasing SHBG and DHT. It also enhanced the expression of testosterone biosynthesis-related proteins and downregulated enzymes associated with testosterone degradation, including 5α-reductase and aromatase. Furthermore, sperm production, motility, and exercise performance improved following FME administration. Overall, FME was found to alleviate LOH symptoms by modulating testosterone metabolism, supporting reproductive and physical health, and maintaining a strong safety profile. These findings provide evidence for the in vivo effectiveness of FME and suggest its potential as a natural therapeutic option for managing LOH and related conditions.