Evidence accumulated suggests that extracellular vesicles (EVs) present in uterine lumen play a role in conceptus-endometrial cell interactions during peri-implantation periods. However, how intrauterine EVs function on endometrium have not been well characterized. To study how intrauterine EVs affect endometrial milieu in cattle, bovine endometrial epithelial cells (EECs) were treated with EVs isolated from uterine flushing fluids (UFs) on day 17 or 20 pregnancy (P17, P20, respectively; conceptus implantation to endometrium begins on days 19-19.5). RNA extracted from EECs were then subjected to RNA sequence analysis. The analysis revealed that transcripts related to immune system were down-regulated in EECs treated with EVs on P20 compared with those on P17. To investigate whether microRNAs (miRNAs) in EVs regulate maternal immune system in the endometrium during the peri-implantation, microRNA sequence and in silico analyses were performed, identifying bta-miR-98 in EVs as a potential miRNA to regulate maternal immune system. Furthermore, the treatment of EECs with bta-miR-98 negatively regulated several immune system-related genes, CTSC, IL6, CASP4 and IKBKE, in EECs. These results suggest that EVs containing bta-miR-98 is a regulator of maternal immune system, possibly allowing the conceptus attachment to the endometrial epithelium during the peri-implantation period.