Increasing evidence suggests that diabetes is associated with an enhanced risk of cognitive decline. The precise mechanisms underlying diabetes-associated cognitive decline (DACD) remain unclear. Here we investigated the molecular changes associated with DACD using a comparative proteomics study of hippocampus in a rat model of type 2 diabetes. In addition, we tested the effects of the Chinese medicine ZiBu PiYin recipe (ZBPYR) on DACD. The hippocampus was dissected from control, diabetic and diabetic rats treated with ZBPYR (DM/ZBPYR). Soluble proteins were separated using fluorescence-based difference gel electrophoresis. Protein spots were visualised with fluorescent dyes and spot density was compared between each pair of groups. Proteins of interest were identified using mass spectrometry. Proteins of specific interest were also tested by western blot and real-time PCR analysis. We found 13 spots that were altered between control and diabetes groups, and 12 spots that were changed between diabetes and DM/ZBPYR groups. The identities of nine proteins were determined by mass spectrometry. The identified proteins were largely involved in energy metabolism, cytoskeleton regulation and oxidative stress. The protein alterations observed in the diabetes group were ameliorated to varying degrees following ZBPYR treatment. The protein changes identified in hippocampus from a rat model of type 2 diabetes suggest that specific cellular alterations contribute to DACD. The Chinese medicine ZBPYR was found to affect multiple targets and partially repaired the original cellular balance. This study may provide important insights into the molecular events underlying DACD and allow the identification of novel therapeutic targets.