Fluctuations in neural activity can produce states that facilitate and accelerate task-related performance. Acquisition of trace eyeblink conditioning (tEBC) in the rabbit is enhanced when trials are contingent on optimal pretrial activity in the hippocampus. Other regions which are essential for whisker-signaled tEBC, such as the cerebellar interpositus nucleus (IPN), somatosensory and prelimbic cortices, may also show optimal connectivity prior to successful performance. Functional magnetic resonance imaging (fMRI) was acquired in nine rabbits during tEBC on the first and tenth days of initial training and once again after a 30-d, training-free hiatus. Data acquired during the intertrial interval was parsed depending on whether or not a conditioned response (CR) occurred on the upcoming trial and seed-based functional connectivity was calculated among the IPN, hippocampus, somatosensory, and prelimbic cortices. Functional connectivity between the left somatosensory cortex and right IPN, regions critical for establishing and producing CRs evoked by right vibrissae vibration and right corneal airpuff, was significantly negative prior to successful, CR trials as compared with unsuccessful, non-CR trials. Differences were not observed for any of the other possible combinations of connectivity. Our results demonstrate that specific pretrial functional connectivity exists within the rabbit brain and differentiates between upcoming behavioral response outcomes. Online analysis of network fluctuations has the potential to be used as the basis for therapeutic interventions to facilitate learning and memory.