Intrinsic connectional architecture of the brain is a crucial element in understanding the governing principle of brain organization. To date, enormous effort has been focused on addressing this issue in humans by combining resting-state functional magnetic resonance imaging (rsfMRI) with other techniques. However, this research area is significantly underexplored in animals, perhaps because of confounding effects of anesthetic agents used in most animal experiments on functional connectivity. To bridge this gap, we have systematically investigated the intrinsic connectional architecture in the rodent brain by using a previously established awake-animal imaging model. First, group independent component analysis was applied to the rsfMRI data to extract elementary functional clusters of the brain. The connectional relationships between these clusters, as evaluated by partial correlation analysis, were then used to construct a graph of whole-brain neural network. This network exhibited the typical features of small-worldness and strong community structures seen in the human brain. Finally, the whole-brain network was segregated into community structures using a graph-based analysis. The results of this work provided a functional atlas of intrinsic connectional architecture of the rat brain at both intraregion and interregion levels. More importantly, the current work revealed that functional networks in rats are organized in a nontrivial manner and conserve fundamental topological properties that are also seen in the human brain. Given the high psychopathological relevance of network organization of the brain, this study demonstrated the feasibility of studying mechanisms and therapies of multiple neurological and psychiatric diseases through translational research.