There is a large gap between diagnostic needs and diagnostic access across much of sub-Saharan Africa, particularly for infectious diseases which inflict a substantial burden of morbidity and mortality. Accurate diagnostics are essential for the correct treatment of individuals and provide vital information underpinning disease surveillance, prevention, and control strategies. Digital molecular diagnostics combine the high sensitivity and specificity of molecular detection with point-of-care format and mobile connectivity. Recent developments in these technologies create an opportunity for a radical transformation of the diagnostic ecosystem. Rather than trying to emulate diagnostic laboratory models in resource-rich settings, African countries have the potential to pioneer new models of healthcare designed around digital diagnostics. This article describes the need for new diagnostic approaches, highlights advances in digital molecular diagnostic technology, and outlines their potential for tackling infectious diseases in sub-Saharan Africa. It then addresses the steps which will be necessary for development and implementation of digital molecular diagnostics. Although the focus is on infectious diseases in sub-Saharan Africa, many of the principles apply to other resource limited settings and to non-communicable diseases.