Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the Fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC); the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. The role of FT stem cells in HGSOC initiation could not be investigated as these cells have not been identified or functionally characterized due to lack of physiologically relevant models. Here, we surmount technical challenges to re-construct the FT stem cell niche in vitro. Using functional approaches as well as bulk and single cell expression analyses, we show that a WNT7A-FZD5 signaling axis is critical for self-renewal of FT stem cells and is regulated by female sex hormones. Single cell expression profiling of reporter organoids identified Wnt/β-catenin Active cells (WβA cells) as a unique cluster of proliferative cells that is enriched in HGSOC markers, particularly CA125; a clinical marker of HGSOC progression and response to therapy. Remarkably, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we propose a first basic description of the nature of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease.