The Stereotaxic Brain Atlas of the Egyptian Fruit Bat provides the first stereotaxic atlas of the brain of the Egyptian fruit bat (Rousettus aegyptiacus), an emerging model in neuroscience. This atlas contains coronal brain sections stained with cresyl violet (Nissl), AChE, and Parvalbumin – all stereotaxically calibrated. It will serve the needs of any neuroscientist who wishes to work with these bats – allowing to precisely target specific brain areas for electrophysiology, optogenetics, pharmacology, and lesioning. More broadly, this atlas will be useful to all neuroscientists working with bats, as it delineates many brain regions that were not delineated so far in any bat species. Finally, this atlas will provide a useful resource for researchers interested in comparative neuroanatomy of the mammalian brain.