Learning and memory employs a series of cognitive processes which require the coordination of multiple areas across the brain. However in vivo imaging of cognitive function has been challenging in rodents. Since these processes involve synchronous firing among different brain loci we explored functional connectivity imaging with resting-state fMRI. After 5-day training on a hidden platform watermaze task, notable signal correlations were seen between the hippocampal CA3 and other structures, including thalamus, septum and cingulate cortex, compared to swim control or naïve animals. The connectivity sustained 7 days after training and was reorganized toward the cortex, consistent with views of memory trace distribution leading to memory consolidation. These data demonstrates that, after a cognitive task, altered functional connectivity can be detected in the subsequently sedated rodent using in vivo imaging. This approach paves the way to understand dynamics of area-dependent distribution processes in animal models of cognition.