Rare diseases (RDs) are individually rare but collectively common, affecting an estimated 1 in 15 individuals in South Africa (SA). Patients with an RD often face a long diagnostic odyssey (>5 years on average) and many obstacles in accessing healthcare. A scoping review was conducted to assess the impact of the COVID-19 pandemic on the SA RD community. Fourteen studies met the inclusion criteria and were explored using thematic analysis, which showed that RD patients were further marginalised during the pandemic, particularly in access to healthcare. Increased inclusivity in policy creation and integrated community-based healthcare are recommended to ensure that RD patients are not an afterthought in future crises.