The Subcortical Maternal Complex (SCMC) is composed of maternally encoded proteins required for the early stages of embryo development. Here we aimed to investigate the expression profile of the genes that encode the individual members of the SCMC in human reproductive failures. To accomplish that, we selected three datasets in the Gene Expression Omnibus repository for differential gene expression (DGE) analysis, comprising human endometrial and placental tissues of patients with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL). The SCMC genes KHDC3L, NLRP2, NLRP4, NLRP5, OOEP, PADI6, TLE6, and ZBED3 were included in the DGE analysis, as well as CFL1 and CFL2 that connect the SCMC with the actin cytoskeleton. Additionally, differential co-expression analysis and systems biology analysis of gene-gene co-expression were performed for KHDC3L, NLRP5, OOEP, and TLE6, demonstrating gene pairs differentially correlated under the two conditions, and the co-expression with genes involved in immune response, cell cycle, DNA damage repair, embryo development, and male reproduction. Compared to control groups, NLRP5 demonstrated upregulation in the endometrium of RIF patients, and KHDC3L was upregulated in the fetal placental tissue of RPL patients, shedding light on the importance of considering SCMC genes in reproductive failures.