Prolonged use of fluoroquinolone class of antibiotics has been studied widely. This class of antibiotic has been reported to have side effects linked to cardiovascular, gastrointestinal and neuronal ramifications following long-term usage. Though the Veterans Affairs has reported a recent drop in antibiotic prescriptions, it is still used in higher number of veterans and use of fluoroquinolones is no exception. Gulf War Illness (GWI) pathology is widely believed to be the result of environmental co-exposures and use of the pyridostigmine bromide pills. Advancing our recent studies on GWI pathology in a mouse model we hypothesized that prolonged use (5 months) of fluoroquinolones coupled with Neomycin might augment poor outcomes in systemic inflammation and neuroinflammation. In this study using a symptom persistence mouse model of GWI, we studied the combinatorial effect of prolonged broad spectrum antibiotic Neomycin and Enrofloxacin treatment for 5 months. Expression of serum proinflammatory cytokine IL-6 saw a sharp increase in mice co-exposed with antibiotics and GW chemicals group (GW-Ab) over GW chemical treated group only (GW). Results also showed decreased expression of blood brain barrier (BBB) tight junction protein Claudin 5 in GW-Ab group when compared to GW group. There was an increased microglial activation, expression of cytokine IL-1β, IL-6 and 3-nitrotyrosine and decreased expression of brain derived neurotrophic factor (BDNF) was also observed in GW-Ab group when compared to GW group. To study whether observed disruption of BBB membrane integrity, increased neuroinflammation had any effect on neurodegeneration and neuroplasticity, we probed the mouse brain for Tau and BDNF receptor expression. Results showed that there was an increased expression of phospho Tau (neurodegenerative marker) and decreased expression of phospho-tropomycin receptor kinase B (TrkB)-receptor of BDNF in GW-Ab group when compared to GW group. Interestingly, elevated expression of glycoprotein 130, a receptor for IL-6 trans signaling was also observed in GW-Ab over GW group. This led us to infer that circulatory IL-6 might be an active mediator in worsening brain pathology observed in GW-Ab, especially since IL-6 has been reported to cross BBB through disruption of tight junction proteins. Mechanistically, studies in mouse astrocytes primed with IL-6 also showed a decreased expression of TrkB with increased expression of Tau protein and further confirmed our in vivo results. Thus we conclude that prolonged antibiotic usage exacerbated GWI-associated neuroinflammation and neurodegeneration in GWI symptom persistence.