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A substantial body of research indicates that spaced training, characterized by longer inter-trial intervals between training epochs, consistently outperforms massed training in promoting durable memory. To investigate the neural mechanisms underlying this difference, we quantified c-Fos expression across 126 brain regions and mapped network activity following both spatial and cue based learning under massed and spaced training protocols. While both training regimens (spaced and massed) and memory types (spatial and cue-based) produced small-world networks with similar overall topology, they differed in the functional organization of specific circuits. Massed spatial training preferentially activated hippocampal–thalamic and claustrum–basal ganglia–thalamic pathways. In contrast, spaced spatial training promoted stronger cortico–thalamic interactions and enhanced communication between the hippocampus and basal ganglia, indicating a shift toward a more integrated, cortically mediated network. These findings suggest that temporal spacing of training reorganizes memory-related brain networks, enhancing cortical, thalamic dynamics to support more efficient spatial memory. Finally, spaced networks were more sensitive to targeted disruptions of key connector hubs–identified through betweenness centrality analysis–than massed networks, pointing to a potential systems-level trade-off.