Abundant in phenolic compounds, “fermented” rooibos herbal tea (FRHT) improves the cognitive performance and exploration of rats, as well as alters the content of monoamines and amino acids in some brain structures. Here, we aim to extend knowledge about the neurochemical and behavioral outcomes of long-term oral FRHT consumption by examining its impact on hypothalamus functions. FRHTs of different leaf-to-water ratios were given to adult male SD rats for 3 months. Their behavior was evaluated in social interaction test. The concentration of hypothalamic monoamines and amino acids was analyzed by HPLC-ECD whereas BDNF/TrkB by Elisa method. It was shown that sustained FRHT consumption did not affect aggression of the rats but was able to increase social deficits, expressed as diminished total time of contact and shorter active social interaction. Upon biochemical investigation, the changes were primarily linked to serotonergic, glutaminergic, and BDNF/TrkB pathway. Decreased 5-HT and TrkB content in the hypothalamus could be linked with social deficits and suggested positive effect on central energy balance, yet the main body mass of animals in the experiment remained unaffected. On the other hand, the reduced hypothalamic serotonin signaling anticipated the influence on hypothalamic–pituitary–adrenal axis and possible diminution of plasma corticosterone level with subsequent behavioral aftermath and lower obesity risk. Our research contributes toward better understanding of the mechanism of action of rooibos tea and its effects within the central nervous system.Graphical abstract