Gulf War Illness (GWI) is a chronic, multi-symptom disorder affecting approximately 30 percent of the nearly 700,000 veterans of the 1991 Persian Gulf War. Recent studies have revealed that GWI-related chemical (GWIC) exposure promotes immune activation and metabolic rewiring, which correlate with neurocognitive impairments and other symptoms of GWI. However, the molecular mechanisms and signaling pathways linking GWIC to inflammation, metabolic alterations, and neurological symptoms remain unclear. Mitochondrial dysfunction has been documented in veterans with GWI and rodent models, and because mitochondria are key immune regulators, we hypothesized that alterations to mitochondria-immune crosstalk could contribute to the development of GWI-related symptoms. Here we show that acute exposure of murine macrophages to GWIC alters mitochondrial respiration and potentiates innate immune signaling and inflammatory cytokine secretion. Using an established mouse model of GWI, we report that neurobehavioral changes, neuroinflammation, and mitochondrial protein rewiring are attenuated in mice lacking the cyclic GMP-AMP synthase (cGAS)-Stimulator of Interferon Genes (STING) and NOD-, LRR- or pyrin domain-containing protein 3 (NLRP3) innate immune pathways. Finally, we report sex differences in response to GWIC, with female mice showing more pronounced cognitive impairment, neuroinflammation, and mitochondrial protein alterations in the brain compared to male mice. Our results provide novel information on sex differences in this model and suggest that STING and NLRP3 are key mediators of the cognitive impairment, inflammation, and mitochondrial dysfunction observed in GWI.