While rotavirus diarrhea has been considered to occur only due to intrinsic intestinal effects within the enteric nervous system, we provide evidence for central nervous system control underlying the clinical symptomology. Our data visualize infection by large-scale three-dimensional (3D) volumetric tissue imaging of a mouse model and demonstrate that rotavirus infection disrupts the homeostasis of the autonomous system by downregulating tyrosine hydroxylase in the noradrenergic sympathetic nervous system in ileum, concomitant with increased intestinal transit. Interestingly, the nervous response was found to occur before the onset of clinical symptoms. In adult infected animals, we found increased pS6 immunoreactivity in the area postrema of the brain stem and decreased phosphorylated STAT5-immunoreactive neurons in the bed nucleus of the stria terminalis, which has been associated with autonomic control, including stress response. Our observations contribute to knowledge of how rotavirus infection induces gut-nerve-brain interaction early in the disease. IMPORTANCE Previous studies have investigated the mechanisms of rotavirus diarrhea mainly by focusing on intrinsic intestinal signaling. Although these observations are compelling and have provided important mechanistic information on rotavirus diarrhea, no information is available on how the gut communicates with the central nervous system (CNS) during rotavirus infection or on how this communication initiates sickness symptoms. We show that rotavirus infection presymptomatically disrupts the autonomic balance by downregulating the noradrenergic sympathetic nervous system in ileum, concomitant with increased intestinal transit and altered CNS activity, particularly in regions associated with autonomic control and stress response. Altogether, these observations reveal that the rotavirus-infected gut communicates with the CNS before the onset of diarrhea, a surprising observation that brings a new understanding of how rotavirus gives rise to sickness symptoms.