Endoplasmic reticulum (ER) stress and unfolded protein response (UPR) participate in stem cell proliferation, differentiation, and apoptosis. Sigma-1 receptor (S1R) is a unique ER chaperon protein that regulates ER stress and UPR. Here, we examine the effects of S1R inhibition on pluripotency and differentiation of human embryonic stem cells (hESCs). hESCs were treated with different doses of an S1R inhibitor (BD 1047), and we investigated the expressions of different pluripotency and lineage-specific genes. The BD-treated hESCs showed increased SRY-box transcription factor 17 (SOX17) expression [definitive endoderm-specific protein], and reductions in NANOG expression and in the number of alkaline phosphatase (ALP)-positive colonies. In silico gene expression analysis of three datasets that contained the hESCs-derived DE samples (GSE98324, GSE63592, GSE52658) was performed to investigate the ER stress-related gene expression patterns during DE differentiation. In silico analysis revealed that UPR-related genes upregulated during DE differentiation and CCL2 was the only gene present in all three DE datasets. qRT-PCR and immunostaining showed that CCL2, eIF2A, ATF4, XBP1, GRP78, DDIT3, DNAJB9, and PDIA5 which are UPR related marker genes were all upregulated in both the BD-treated hESCs and female and male hESC-derived DE cells. The results of this study suggest possible roles for S1R, ER stress-related genes, and the CCL2 pathway during differentiation of hESCs into DE. These potential new targets may improve the efficiency of protocols used to differentiate endodermal lineages.