The use of functional magnetic resonance imaging (fMRI) to measure spontaneous fluctuations in blood oxygen level dependent (BOLD) signals has become an indispensable tool to investigate how brain regions interact and form long-range networks. Statistical dependency measures between brain regions obtained from BOLD signals can inform about brain functional states in longitudinal studies of neurological and psychiatric disorders. Furthermore, its non-invasive nature allows comparable measurements in clinical and animal studies, providing excellent translational capabilities. In the present study, we apply Network-Based Statistic (NBS) to investigate alterations in the functional connectivity (FC) of the rat brain in a post-dependent (PD) state, an established animal model of clinical relevant features in alcoholism. In contrast to mass-univariate tests, in which comparisons are performed at single link-level, NBS enhances the statistical power by assuming that the connections comprising the effect of interest are interconnected. Brain-wide resting-state fMRI signals were collected in 14 controls and 13 PD rats, and Pearson correlations computed between 47 brain regions of interest (ROIs). The NBS analysis revealed statistically significant differences in a connected network of structures including hippocampus, amygdala, lateral hypothalamus and the raphe nucleus, all regions with known relevance for addictive behaviors. In contrast, no individual connection could be found significant by univariate comparisons with false discovery rate (FDR) correction. Correlations between the structures in the identified subnetwork tend to decrease or become negative (anti-correlated) in the PD state compared to controls. We interpret this result as evidence for a disconnected subnetwork in the PD state.