Objective The current study was performed to investigate isobaric tags for relative and absolute quantitation ( iTRAQ)-based quantitative proteomic analysis of the amygdala in rats with complete Freund’ s adjuvant (CFA)-induced chronic pain. A comprehensive analysis of protein expression was performed to explore the underlying mechanism by which electroacupuncture (EA) affects chronic pain. Methods Twenty-seven male Sprague-Dawley ( SD) rats were randomly divided into a control group (control group), model group and EA-treated group (EA group), with 9 rats in each group. Inflammatory pain was induced with an intraplantar injection of 100 μL CFA into the plantar surface of the left hind paw of the male SD rats. EA stimulation of the bilateral Zusanli and Sanyinjiao acupoints was performed for 14 days. Based on iTRAQ-based proteomics analysis, we investigated protein expression in the amygdala. Results EA increased the paw withdrawal thresholds (PWTs) in rats with inflammatory pain induced by noxious stimulation. A total of 6319 proteins were quantified in the amygdala. Of these identified proteins, 58 significantly altered proteins were identified in the model group compared with the con group, and 37 were identified in the EA group compared with the con group. Three proteins were found to be differentially expressed in the amygdala of model rats and EA-treated rats. Conclusions Our study confirms the possible mechanism underlying the effects of EA on the amygdala in rats with chronic pain.