We report on the faunal transition of benthic foraminifera during the middle Eocene at Site U1333 (4862 m water depth, 3,560–3,720 m paleo-water depth) of Integrated Ocean Drilling Program Expedition 320 in the eastern equatorial Pacific Ocean. During the period ∼41.5–40.7 Ma, which includes carbonate accumulation event 3 (CAE-3), the benthic foraminiferal accumulation rate (BFAR) increased gradually and then it declined rapidly. In contrast, BFAR was considerably lower during ∼40.7–39.4 Ma, corresponding to the middle Eocene climatic optimum (MECO), and then it increased during ∼39.3–38.4 Ma, including CAE-4. Diversity (E [S200]) was slightly lower in the upper part of the study interval than in the lower part. The most common benthic foraminifera were Nuttallides truempyi, Oridorsalis umbonatus, and Gyroidinoides spp. in association with Globocassidulina globosa and Cibicidoides grimsdalei during the period studied. Quadrimorphina profunda occurred abundantly with N. truempyi, O. umbonatus, and G. globosa during ∼39.4–38.4 Ma, including CAE-4, although this species was also relatively common in the lower part of the study interval. Virgulinopsis navarroanus and Fursenkoina sp. A, morphologically infaunal taxa, were common during ∼38.8–38.4 Ma, corresponding to the late stage of CAE-4. Based on Q-mode cluster analysis, four sample clusters were recognized and their stratigraphic distributions were generally discriminated in the lower and upper parts of the study interval. Thus, there was only a small faunal transition in the abyssal eastern equatorial Pacific during the middle to late-middle Eocene. The faunal transition recognized in this study may be related to recovery processes following intense carbonate corrosiveness in the eastern equatorial Pacific during MECO.