The lemon flavonoid extract Eriomin® (LE), which is rich in eriocitrin, has demonstrated antioxidant and anti-inflammatory properties in both animal and human studies. Given the established interplay among aging, oxidative stress, and inflammation, this study investigated the influences of LE on the pituitary–adrenal (PA) axis in aged rats and its potential to mitigate age-related physiological changes in this system. The effects of LE (40 mg/kg/day suspended in sunflower oil) on the morphofunctional properties of the PA axis were studied in 24-month-old male Wistar rats following four weeks of oral treatment. Control groups included vehicle-treated (sunflower oil; CON) and untreated intact controls (ICON). Stereological and imaging analyses revealed no significant changes in pituitary ACTH cells; however, Pomc gene expression was significantly downregulated in the LE group compared to both controls (p ≤ 0.05). LE treatment resulted in a significant reduction in adrenal gland weight (p ≤ 0.05), adrenal gland volume (p ≤ 0.01), zona fasciculata (ZF) volume (p ≤ 0.01) and ZF cell volume (p ≤ 0.05). These changes were accompanied by a significant decrease in serum corticosterone levels (p ≤ 0.05). In conclusion, LE downregulated PA axis activity in aged rats. Considering the association between age-related increases in PA activity and adverse health outcomes, citrus flavonoid extracts such as LE may hold promise as anti-aging supplements aimed at mitigating age-related stress dysregulation.