In just twenty years, humanity has progressed from the first sequenced human genome to the ability to sequence one in a matter of hours and for only hundreds of dollars. This rise in affordability and speed has enabled physicians to use whole genome sequencing (WGS) as a diagnostic tool, particularly in cases of rare disease in pediatric patients where it has already demonstrated immense potential. However, such a rapid development in technology powerful enough to unlock a person’s genetic information has also led to necessary questions regarding when and how it is applied. In this assessment, we discuss the implications of WGS adoption in pediatric healthcare, focusing specifically on ensuring ethical and equitable collection and communication of genomic data as well as the need for secure and accessible data storage methods. We identify several key areas where further policy is most pressing and provide value-driven recommendations centered on guaranteeing pediatric patient safety, equity, and empowerment during the broader introduction of WGS tools. In particular, we advocate for legal frameworks that limit present usage of WGS to only those patients with a clear and present need, guidelines that expand the labor force that can conduct WGS, increasing access and equity, improved standards for storage, access, and sharing of WGS data, and finally expanding Medicaid coverage to include WGS use in critical care settings.