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Extracellular glypicans play pivotal roles in organogenesis, stem cell maintenance and cancer development. However, the growth phenotypes associated with different levels of glypican are not consistent in development or tumorigenesis. This requires clarification on how the spatial patterns of glypican relate to the distribution of signaling molecules in different cellular contexts, and how glypican expression is regulated. We have previously reported that Dally, one of the glypican members in Drosophila, is required in the niche for the maintenance of germline stem cells (GSCs) via short-range BMP signaling in ovary. However, the regulatory mechanism of glypican pattern in the ovarian stem cell niche remains elusive. Our current data demonstrate that the Notch pathway is genetically upstream of Dally and its function to maintain GSCs relies on Dally expression. Combining yeast and fruit fly genetics, we illustrate that Dally is under the transcriptional control of Notch signaling via the transcription factor Su(H). Further, we assayed human glypicans and disease-associated variants in Drosophila ovary, which can serve as an effective system to evaluate the structure–function relationship of human homologs.