Functional coupling networks are widely used to characterize collective patterns of activity in neural populations. Here, we ask whether functional couplings reflect the subtle changes, such as in physiological interactions, believed to take place during learning. We infer functional network models reproducing the spiking activity of simultaneously recorded neurons in prefrontal cortex (PFC) of rats, during the performance of a cross-modal rule shift task (task epoch), and during preceding and following sleep epochs. A large-scale study of the 96 recorded sessions allows us to detect, in about 20% of sessions, effective plasticity between the sleep epochs. These coupling modifications are correlated with the coupling values in the task epoch, and are supported by a small subset of the recorded neurons, which we identify by means of an automatized procedure. These potentiated groups increase their coativation frequency in the spiking data between the two sleep epochs, and, hence, participate to putative experience-related cell assemblies. Study of the reactivation dynamics of the potentiated groups suggests a possible connection with behavioral learning. Reactivation is largely driven by hippocampal ripple events when the rule is not yet learned, and may be much more autonomous, and presumably sustained by the potentiated PFC network, when learning is consolidated. Author Summary Cell assemblies coding for memories are widely believed to emerge through synaptic modification resulting from learning, yet their identification from activity is very arduous. We propose a functional-connectivity-based approach to identify experience-related cell assemblies from multielectrode recordings in vivo, and apply it to the prefrontal cortex activity of rats recorded during a task epoch and the preceding and following sleep epochs. We infer functional couplings between the recorded cells in each epoch. Comparisons of the functional coupling networks across the epochs allow us to identify effective potentiation between the two sleep epochs. The neurons supporting these potentiated interactions strongly coactivate during the task and subsequent sleep epochs, but not in the preceding sleep, and, hence, presumably belong to an experience-related cell assembly. Study of the reactivation of this assembly in response to hippocampal ripple inputs suggests possible relations between the stage of behavorial learning and memory consolidation mechanisms.