The present study aimed to evaluate the effect of E-VCO on the neurobehaviour and intestinal health parameters of obesity-induced rats, focusing on food consumption, body composition, bacterial and faecal organic acids and histological analyses in the hippocampus and colon. A total of 32 male Wistar rats were randomized into healthy (HG, n = 16) and obese groups (OG, n = 16), which consumed a control or cafeteria diet for eight weeks, respectively. After this period, they were subdivided into four groups: healthy (HG, n = 8); healthy treated with E-VCO (HGCO, n = 8); obese (OG, n = 8); obese treated with E-VCO (OGCO, n = 8), continuing for another eight weeks with their respective diets. The treated groups received 3000 mg kg-1 of E-VCO and control groups received water via gavage. Food preference, body weight gain, body composition, anxiety- and depression-like behaviour were evaluated. Bacteria and organic acids were evaluated in faeces, and histological analyses of the hippocampus and M1 and M2 macrophages in the colon were performed. E-VCO reduced energy intake (16.68%) and body weight gain (16%), although it did not reduce the fat mass of obese rats. E-VCO showed an antidepressant effect, increased lactic acid bacteria counts and modulated organic acids in obese rats. Furthermore, E-VCO protected the hippocampus from neuronal degeneration caused by the obesogenic diet, decreased the M1 macrophage and increased the M2 macrophage population in the gut. The results suggest neurobehavioural modulation and improved gut health by E-VCO, with promising effects against obesity-related comorbidities.