Endometrial receptivity is a prerequisite for successful embryo implantation and pregnancy. Receptivity involves complex processes promoted by many transcripts that are key components of molecular pathways that depend on ovarian hormones and that contribute to shaping structural, metabolic, and communication properties of endometrial cells toward reception of embryos. MicroRNAs (miRNAs) are important regulators of the expression of these transcripts encoding effector molecules. We acquired miRNA and mRNA signatures, miRNA-mRNA pairs, and regulatory networks linked with the emergence and maintenance of postimplantation pregnancy. Endometrial tissue samples were obtained at Days 3 and 7 of the estrous cycle of cows that did or did not become pregnant after transfer of either in vivo-produced (IVV) or in vitro-produced (IVT) embryos in the next cycle following the biopsy. We report a list of endometrial miRNAs that were differentially expressed between Day 3 and Day 7 of the bovine estrous cycle (including miR-1290, miR-3437, miR-1246, miR-486, miR-3107, and miR-382), that differed with high or low endometrial receptivity (miR-3902-3p, miR-1825, miR-H14-3p, miR-885-3p, miR-504-3p, and miR-186), or that differed among the IVT and IVV transfers (miR-449a/b/c, miR-138, miR-874, miR-4342, miR-2231, and miR-2751). Moreover, mRNA transcripts were also analyzed, and pairs of negatively correlated miRNAs and mRNAs were predicted in silico. The miRNA-mRNA target pairs had roles in response to hormonal stimuli and oxidative stress, chromatin organization, miRNA-mediated epigenetic histone changes, cell proliferation, p53 signaling, and apoptosis. Overall, we identified significant miRNAs, miRNA-mRNA pairs, and functional networks that are associated with the state of pregnancy at Day 28 as a parameter of endometrial receptivity and that are affected by estrous cycle and embryo culture systems.