Memory formation is an essential function for survival and cognitive flexibility that involves both synaptic and systems consolidation. The latter is an intricate process requiring integrated signalling inputs into complex neural networks over time. The purpose of the present study was to identify proteins and pathways affected by memory formation induced by the conditioned lick suppression paradigm, as well as to investigate the role of the dHF in the transfer of memory to a more permanent mode in other brain areas. To evaluate the acquisition of fear memory, a protocol of conditioned suppression of an ongoing behaviour was conducted for either 8 or 46 days. Two or 40 days after conditioning, the animals were subjected to a retention test and were then euthanized after 24 hours for dHF harvesting. There were 1,165 proteins identified and 265 quantified. The analysis of the fear memory performed on post-conditioning day 2 showed an upregulation of 5 proteins and a downregulation of 11 proteins. Additionally, an analysis on post-conditioning day 40 showed that 8 proteins were upregulated, and 32 proteins were downregulated. Integrated pathway analysis of the proteomics data indicated changes in the myelin sheath, neuron generation and differentiation, regulation of neurogenesis and synaptic vesicle transport, axonal development and the growth cone. Altogether, the current findings provide further support for the role of the dHF in conditioned lick suppression memory and novel insights into the molecular changes that are correlated with the transfer of memory from the dHF to other cortical areas, which may be a target for cognitive enhancers.