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Abstract State‐level newborn screening allows for early treatment of genetic disorders, which can substantially improve health outcomes for newborns. As the cost of genetic testing decreases, it is becoming an essential part of newborn screening. A genetic disorder can be caused by many mutation variants; therefore, an important decision is to determine which variants to search for (ie, thepaneldesign), under a testing budget. The frequency of variants that cause a disorder and the incidence of the disorder vary by racial/ethnic group. Consequently, it is important to consider equity issues in panel design, so as to reduce disparities among different groups. We study the panel design problem using cystic fibrosis (CF) as a model disorder, considering the trade‐offs between equity and accuracy, under a limited budget. Most states use a genetic test in their CF screening protocol, but panel designs vary, and, due to cost, no state's panel includes all CF‐causing variants. We develop models that design equitable genetic testing panels, and compare them with panels that maximize sensitivity in the general population. Our case study, based on realistic CF data, highlights the value of equitable panels and provides important insight for newborn screening practices.