Cas9-mediated gene editing of hematopoietic stem cells (HSCs) has great potential for functional studies and gene therapies. Current gene delivery methods, such as viral transduction or electroporation face challenges in clinically relevant parameters, such as efficiency, cell function and viability. We show that nanostraws can be used as an alternative method to deliver small molecules and mRNA to human hematopoietic stem and progenitor cells (HSPCs) without affecting cell viability or colony forming potential. Nanostraws are hollow alumina nanotubes on a polymer membrane, that pierce and connect cultured cells in their native medium with a liquid compartment that contains the cargo of interest. The cargo is delivered into the cells by diffusion or under the influence of a weak electric field. Nanostraws have previously been used to deliver small molecules, mRNA, and proteins to adherent cell lines with high efficiency and low toxicity. We demonstrate that they can also be used to deliver cargo to non-adherent, primary human HSPCs by centrifuging them onto the nanostraws to facilitate close contact and cell-membrane penetration. By applying a pulsed electric field, we delivered propidium iodide and GFP mRNA to more than 75% of treated cells. Treatment with our method did not affect cell viability, proliferative capacity, and colony forming potential, while cells that were treated with conventional electroporation were strongly impaired in these parameters. Further, we used nanostraws to deliver Cas9 mRNA to CD34+ cells and demonstrate successful editing of the CD45 gene. This approach can thus be used to facilitate CRISPR/Cas9 gene editing in primary human HSPCs. Our results highlight that nanostraw mediated cargo delivery is a non-toxic alternative to established methods, with distinct advantages that can be relevant for functional studies and clinical applications.