The definition of homology and its application to reproductive structures, external genitalia, and the physiology of sexual pleasure has a tortuous history. While nowadays there is a consensus on the developmental homology of genital and reproductive systems, there is no agreement on the physiological translation, or the evolutionary origination and roles, of these structural correspondences and their divergent histories. This paper analyzes the impact of evolutionary perspectives on the homology concept as applied to the female orgasm, and their consequences for the biological and social understanding of female sexuality and reproduction. After a survey of the history of pre‐evolutionary biomedical views on sexual difference and sexual pleasure, we examine how the concept of sexual homology was shaped in the new phylogenetic framework of the late 19th century. We then analyse the debates on the anatomical locus of female pleasure at the crossroads of theories of sexual evolution and new scientific discourses in psychoanalysis and sex studies. Moving back to evolutionary biology, we explore the consequences of neglecting homology in adaptive explanations of the female orgasm. The last two sections investigate the role played by different articulations of the homology concept in evolutionary developmental explanations of the origin and evolution of the female orgasm. These include the role of sexual, developmental homology in the byproduct hypothesis, and a more recent hypothesis where a phylogenetic, physiological concept of homology is used to account for the origination of the female orgasm. We conclude with a brief discussion on the social implications for the understanding of female pleasure derived from these different homology frameworks.