Human PSCs offer tremendous potential for both basic biology and cell‐based therapies for a wide variety of diseases. The ability to manipulate the genome of these cells using the CRISPR‐Cas9 technology has expanded this potential by providing a valuable tool for engineering or correcting disease‐associated mutations. Because of the high efficiency with which CRISPR‐Cas9 creates targeted double‐strand breaks, a major challenge has been the introduction of precise genetic modifications on one allele, without indel formation on the non‐targeted allele. To overcome this obstacle, we describe the use of two oligonucleotides, one expressing the sequence change, with the other maintaining the normal sequence. In addition, we have streamlined both the transfection and screening methodology to make this protocol efficient with small numbers of cells and to limit the amount of labor‐intensive clone passaging. This protocol provides a streamlined and technically simple approach for generating valuable tools to model human disease in stem cells. © 2018 by John Wiley & Sons, Inc.