Substantial evidence from previous studies has suggested an association between major depressive disorder (MDD) and inflammation, and previous studies have associated prefrontal cortex (PFC) dysfunction with MDD. Systemic administration of bacterial lipopolysaccharide has been used to study inflammation-associated behavioral changes in rodents. However, proteomic studies investigating PFC protein expression in an LPS-induced mouse model of depression have yet to be conducted. Using two-dimensional electrophoresis coupled with matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry, PFC proteomes were comparatively assessed in LPS-induced acute inflammation reaction mice, LPS-induced depressive-like behavior mice (Dep), and control mice. A total of 26 differentially expressed proteins were identified, two of which were selected for western blot analysis, the results of which revealed a significant increase in the expression levels of creatine kinase B and dihydropyrimidinase-like 3 in Dep mice, suggesting that changes in energy metabolism and neuro-genesis occur in the PFC of Dep mice. Further investigation on these processes and on the proteins of the PFC are required in order to elucidate the pathophysiological mechanism underlying MDD.