<p>Chikungunya virus (CHIKV) infection, a neglected tropical disease causes severe morbid symptoms that can be persistent and debilitating. CHIKV mediated pathogenesis is a complex combination of host and viral factors that results in immune responses causing incapacitating symptoms. A significant player of disease development is tumor necrosis factor-α (TNF-α), the villain responsible for unremitting inflammation and disease pathogenesis. This study explored the potential of TNF-α dysregulation that can enhance CHIKV mediated disease development along with the prospective of ultradiluted hydroethanolic preparation of <i>Eupatorium perfoliatum</i> to limit the symptoms. In silico molecular docking studies revealed that&#xa0;<i>Eupatorium perfoliatum</i> has strong molecular interactions with TNF-α. To substantiate the results, in vivo transcriptional and translational quantification of TNF-α by qRT-PCR and immunohistochemistry before and after treatment with candidate medicine was performed which produced similar outcome. Macroscopic and histology results also revealed neuropathogenesis and muscle waste caused by CHIKV infection and a systemic lowering of the same after treatment. Hub genes of TNF-α were analyzed to identify the other probable players that can augment CHIKV mediated pathogenesis. qRT-PCR results showed that the candidate medicine could lower the transcriptional overexpression of the hub genes thereby lowering disease pathogenesis. In vitro cytopathic effects upon infection were also lowered by the candidate medicine. Therefore, this study helps not only to recognize the possible villainous role of TNF-α but to also identify novel therapeutic markers of CHIKV mediated disease development by hub gene analysis and the potential of the alternative medicine, ultradiluted <i>Eupatorium perfoliatum</i> in lowering the same.</p> Graphical Abstract <p></p>