The existence of repeat breeder cows (RBCs) causes low reproductive performance. The causes of RBCs include low-quality oocytes and embryos, hormonal dysregulation, and unsuitable uterine environments. To improve unsuitable uterine conditions for RBCs, we focused on nobiletin (NOB), a natural citrus flavone with various beneficial roles. The role of NOB in bovine endometrial epithelial cells (BEECs) was examined. An analysis of BEECs showed that gene expression and altered pathways differed between the control and NOB treatment, with NOB regulating the pathways of steroid biosynthesis, lysosomal function, and inflammatory responses. NOB treatment significantly increased the number and activation of endosomes and lysosomes in BEECs. Moreover, we performed phagocytosis assays using fluorescence-conjugated lipopolysaccharide (LPS) with lysosomes in NOB-treated BEECs, which resulted in an increase in the co-localization of phagocytosed LPS with lysosomes. NOB treatment stimulated the mRNA expression of various lysosomal hydrolases, including cathepsin B and cathepsin K, and suppressed the gene expression of cytokines in inflammation-associated pathways (rheumatoid arthritis, the IL-17 signaling pathway, etc.). NOB significantly suppressed the LPS-induced mRNA expression of the inflammatory cytokine IL-8 and its secretion in BEECs. In conclusion, NOB activates the endosome–lysosomal system via phagocytosis to eliminate the bacterial component LPS and suppress inflammatory responses to defense mechanisms in BEECs.