The transcriptional regulation of neural stem/progenitor cells (NS/PCs) is of great interest in neural development and stem cell biology. The RNA-binding protein Musashi1 (Msi1), which is often employed as a marker for NS/PCs, regulates Notch signaling to maintain NS/PCs in undifferentiated states by the translational repression of Numb expression. Considering these critical roles of Msi1 in the maintenance of NS/PCs, it is extremely important to elucidate the regulatory mechanisms by which Msi1 is selectively expressed in these cells. However, the mechanism regulating Msi1 transcription is unclear. We previously reported that the transcriptional regulatory region of Msi1 is located in the sixth intron of the Msi1 locus in NS/PCs, based on in vitro experiments. In the present study, we generated reporter transgenic mice for the sixth intronic Msi1 enhancer (Msi1-6IE), which show the reporter expression corresponding with endogenous Msi1-positive cells in developing and adult NS/PCs. We found that the core element responsible for this reporter gene activity includes palindromic Regulatory factor X (Rfx) binding sites and that Msi1-6IE was activated by Rfx. Rfx4, which was highly expressed in NS/PCs positive for the Msi1-6IE reporter, bound to this region, and both of the palindromic Rfx binding sites were required for the transactivation of Msi1-6IE. Furthermore, ectopic Rfx4 expression in the developing mouse cerebral cortex transactivates Msi1 expression in the intermediate zone. This study suggests that ciliogenic Rfx transcription factors regulate Msi1 expression through Msi1-6IE in NS/PCs.