Sickness behaviour, fever, anxiety, anorexia and depression are interrelated phenomena. The citrus fruit peels offering significant low-cost nutritional dietary supplements due to its rejuvenating biological activities. The present study was undertaken to explore the beneficial effect of enriched phenolic fraction of peel (PFMC) in lipopolysaccharide (LPS)-induced sickness behaviour and anorexia in mice. Further, the HPTLC estimation of hesperidin, total phenolic and flavonoid content in PFMC were carried out. In silico molecular docking and dynamic studies of bioactive compounds against NF-κB (1NFK) were also performed. The amount of hesperidin was found to be 55.33 mg/g of PFCM as per the proposed HPTLC method. Total phenolic and flavonoid content was found to be 71 mg of gallic acid/g and 58.1 mg of quercetin/g of PFCM. The single dose of LPS (400 μg/kg, i.p) treatment exhibited significant reduction in food, water intake and behavioural tests and tissue GSH, whereas significantly higher levels of tissue LPO and plasma IL-6 levels compared to normal control. Pre-treatment of PFCM (100 and 200 mg/kg, i.p) and dexamethasone (1 mg/kg, i.p) showed significantly altered the LPS-induced behavioural, anorexia and biochemical parameters. The bioactive compounds such as hesperidin, naringenine, naringin and dexamethasone showed docking score of −22.49, −21.99, −16.43 and −11.12 respectively against NF-κB (1NFK). Among tested bioactive compounds, naringin clearly exhibited higher inhibiting property on target protein structure. The protective effect of PFCM in LPS-induced anorexia and sickness behaviour is due to its antioxidant, anti-inflammatory and appetizing activities, inhibiting IL-6 and NF-κB.