Eukaryotic translation initiation factor 2, subunit 3, and structural gene Y-linked (EIF2S3Y) is essential for spermatogenesis in mouse models. However, its effect on embryonic stem (ES) cells remains unknown. In our observation, differentiated ES cells showed higher levels of EIF2S3Y. To further elucidate its role in ES cells, we utilized ES-derived EIF2S3Y-overexpressing cells and found that EIF2S3Y down-regulated the pluripotency state of ES cells, which might be explained by decreased histone methylation levels because of reduced levels of ten-eleven translocation 1 (TET1). Moreover, EIF2S3Y-overexpressing cells showed an enhanced proliferation rate, which might be due to increased Cyclin A and Cyclin E levels. This study highlighted novel roles of EIF2S3Y in the pluripotency maintenance and proliferation control of ES cells, which would provide an efficient model to study germ cell generation as well as cancer development using ES cells, thus providing valuable target for clinical applications of ES cells.