Neural stem cells (NSCs) are essential for the generation of new neurons and also exert regulatory functions within their niche. NSCs are altered in many pathological conditions, and their role as a therapeutic target is being increasingly studied. Isolating a pure population of NSCs from the brain is challenging due to the lack of unique biomarkers. The development of transgenic mouse lines in which NSCs express fluorescent proteins has been greatly helpful, but these resources are sometimes unavailable to many research groups worldwide. Herein, we detail protocols for isolating NSCs from the adult brain using fluorescence-activated cell sorting (FACS) from both transgenic and non-transgenic mice. By utilizing fluorescence-conjugated antibodies targeting unique cell surface markers, a flow cytometer can distinguish different cell types based on their characteristic fluorescence profiles. This method enables precise sorting of cells according to their phenotype, facilitating in-depth exploration of cellular diversity and functionality.