Human pluripotent stem cells (hPSCs) have been used to derive self-renewing neural progenitor (NP) cell lines. Here we describe methods to genetically modify these cells. Detailed methods for transfection and nucleofection in PSC-derived NP cells are presented. We have shown that nucleofection results in higher yield of GFP(+) NP cells as compared with transfection. However, nucleofection leads to higher cell death than transfection. Application of these methods allows for the development of novel tools to study human development and cellular differentiation. Genetically modified NPs have direct application in neural imaging, tracking neural cells, and for drug delivery to target organs using neural progenitor cells as carriers.