Between 2017 and 2022, the U.S. Supreme Court examined three cases that involved states that tried to limit the use of public money to support religious-affiliated schools. The Supreme Court found a violation of the Free Exercise Clause in all three cases. Although not the focus of the Court's opinions, these cases may have created avenues for discriminatory practices in publicly funded state school voucher programs. In elevating free-exercise rights above Establishment Clause concerns, the Court's decisions may have serious implications for students' civil rights in schools. This article specifically examines whether the growth of school voucher programs in the context of these recent Supreme Court decisions creates a pathway for racial discrimination in participating voucher schools. We first explore the impact of the three Supreme Court decisions. Specifically, we argue that when the Court eliminated distinctions between policies denying funding because of religious status and policies denying funding for religious uses and when it elevated free-exercise arguments, it may have opened additional avenues for discrimination. Thus, we next address whether participating voucher schools can refuse admission to Black students. To set the context for this discussion, we provide a brief historical analysis of case law that has previously supported race-based discrimination on religious grounds. We show that although past court cases and federal tax policy have created a bulwark against such discrimination, the recent rulings favoring free exercise rights raise concerns. If free-exercise rights trump civil rights, some voucher statutes may create an alternative funding stream for modern-day "segregation academies."