Characterizing the nature and underlying neurobiological causes of psychiatric and neurological diseases at the circuit and network levels has remained elusive and necessitates the use of robust animal models. Noninvasive functional magnetic resonance imaging allows systems-level insight into disease phenotype in humans and animals alike, and functional neuroimaging represents an ideal platform for translational and reverse-translational research, with common measurements collected across species. Animal neuroimaging allows invasive manipulations and conveniently bypasses many limitations associated with human subjects; however, awake animal imaging introduces its own constraints to reduce motion and limit subjective stress. Anesthetics offer a viable alternative, but the pharmacodynamics, pharmacokinetics, and molecular targets of anesthetics and their effects on physiology, neural activity, and neurovascular coupling must be considered. We discuss the physiological basis of and the influence of anesthetics on neurovascular coupling. We discuss anesthetic use in functional magnetic resonance imaging and focus on an anesthetic protocol developed in our laboratory. Finally, we discuss in detail our most recent work examining the physiological basis of resting-state functional magnetic resonance imaging using this anesthetic regimen and the future directions of animal neuroimaging research. Using animal imaging in combination with cutting-edge in vivo neuromodulatory techniques is essential for causal understanding of brain function in health and disease and offers an exemplary bridge between human and animal research studies.