Alcohol use disorders (AUD) are a major public health concern. Understanding the brain network alterations is of the utmost importance to diagnose and develop treatment strategies. Employing resting-state functional magnetic resonance imaging, we have performed a longitudinal study in a rat model of chronic excessive alcohol consumption, to identify functional alterations in brain networks triggered by alcohol drinking. Two time points were considered: 1) before alcohol consumption (control condition) and 2) after 30 days of alcohol drinking (alcohol condition). We first identified nine resting-state networks with group independent component analysis. Afterwards, dual regression was applied to obtain subject-specific time courses and spatial maps. L2-regularized partial correlation analysis between pairs of networks showed that functional connectivity (FC) between the retrosplenial-visual and striatal networks decreases due to alcohol consumption, whereas FC between the prefrontal-cingulate and striatal networks increases. Analysis of subject-specific spatial maps revealed FC decreases within networks after alcohol drinking, including the striatal, motor-parietal, prefrontal-cingulate, retrosplenial-visual and left motor-parietal networks. Overall, our results unveil a generalized decrease in brain FC induced by alcohol drinking in genetically predisposed animals, even after a relatively short period of exposure (1 month). The only exception to this hypo-connectivity state is the functional association between the striatal and prefrontal-cingulate networks, which increases after drinking, supporting evidence in human alcoholics.