An estimated one-third of American veterans of the 1991 Gulf War continue to experience multiple unexplained health problems known as Gulf War Illness (GWI). GWI is a chronic disorder that is characterized by persistent and heterogeneous symptoms including but not limited to anxiety, pain, fatigue, and cognitive impairment. In the current study, we hypothesized that exposure to toxic chemicals during the Gulf War (GW) may produce a long-lasting disruption in the endocannabinoid (ECB) system, one of the brain’s endogenous anti-inflammatory mechanisms, leading to dysregulated microglial activation and contributing to GWI pathogenesis. Using the mice model for GWI, we found that levels of the main ECB molecule, anandamide, are significantly reduced in the brain of GWI model mice, when compared to vehicle-injected control mice. In addition, the transcription of Faah, which encodes the enzyme that inactivates anandamide, fatty acid amide hydrolase (FAAH), was significant elevated in the prefrontal cortex of the GWI mice. Importantly, pharmacological normalization of the ECB deficit through administration of the FAAH inhibitor, URB597, recovered brain anandamide levels and corrected behavioral abnormalities of the GWI model mice. Furthermore, GWI mice displayed unexpected changes in microglial transcriptome, implying dysfunctional regulation of their innate immune function.Our results suggest that exposure to GW chemicals may induce a deficit in the brain ECB system that are associated with persistent alteration in microglial functions. Behavioral abnormalities of the model mice were rescued by pharmacological normalization of the ECB system, which may serve as an effective therapeutic strategy for ameliorating GWI symptomology.