Recently, cyclic peptide drugs have attracted much attention because they can aim targets such as intracellular protein-protein interactions that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. However, cyclic peptides generally have the disadvantage of low membrane permeability. This remains a major challenge in the development of peptide drugs that can be orally administered and inhibit intracellular targets. Although there were many studies measuring the permeability of cyclic peptides, a comprehensive database that brings together these data in a unified format is not yet available. Therefore, this study collected a total of 7334 cyclic peptide structure and experimentally measured membrane permeability data comprehensively from 45 papers and 2 pharmaceutical company patents. We compiled them into CycPeptMPDB(http://cycpeptmpdb.com), the world's first cyclic peptide membrane permeability database. To unambiguously represent structures of cyclic peptides, which are more complex than small-molecule compounds, CycPeptMPDB also contains a unified sequence representation of all peptides generated using the HELM notation. In addition to basic data storage, CycPeptMPDB provides several supporting functions such as searching, data analysis, and downloading.