The study introduces the Human Endometrial Cell Atlas (HECA), a high-resolution single-cell reference atlas that integrates published and new endometrial single-cell transcriptomics datasets from 63 women with and without endometriosis. The HECA assigns consensus and identifies previously unreported cell types, validated using spatial transcriptomics and an independent single-nuclei dataset. Key findings include the identification of an epithelial *CDH2*^+^ population in the basalis and distinct populations of functionalis epithelial and stromal cells. The atlas provides insights into stromal-epithelial cell coordination via TGFβ signaling and signaling between fibroblasts and an epithelial population expressing progenitor markers in the basalis. Integration with large-scale endometriosis genome-wide association study data highlights decidualized stromal cells and macrophages as likely dysregulated in endometriosis. The HECA is a valuable resource for studying endometrial physiology and disorders and guiding microphysiological in vitro systems development.The study introduces the Human Endometrial Cell Atlas (HECA), a high-resolution single-cell reference atlas that integrates published and new endometrial single-cell transcriptomics datasets from 63 women with and without endometriosis. The HECA assigns consensus and identifies previously unreported cell types, validated using spatial transcriptomics and an independent single-nuclei dataset. Key findings include the identification of an epithelial *CDH2*^+^ population in the basalis and distinct populations of functionalis epithelial and stromal cells. The atlas provides insights into stromal-epithelial cell coordination via TGFβ signaling and signaling between fibroblasts and an epithelial population expressing progenitor markers in the basalis. Integration with large-scale endometriosis genome-wide association study data highlights decidualized stromal cells and macrophages as likely dysregulated in endometriosis. The HECA is a valuable resource for studying endometrial physiology and disorders and guiding microphysiological in vitro systems development.