This paper critically assesses the prospects and limitations of Africa’s Small Island Developing States (SIDS)—Cape Verde, Comoros, Madagascar, Mauritius, São Tomé and Príncipe, and Seychelles—within the framework of the African Continental Free Trade Area (AfCFTA). Despite the AfCFTA’s potential to enhance intra-African trade, reduce barriers, and foster economic integration, African SIDS face structural challenges that inhibit their full participation. These include geographic remoteness, limited economies of scale, narrow export bases, underdeveloped infrastructure, and heightened climate vulnerability. Through a comparative analysis, the study reveals significant disparities in institutional capacity, regional connectivity, and integration readiness across the island states. The paper argues for the implementation of targeted interventions such as flexible rules of origin, accelerated liberalisation of services, strategic infrastructure investment, and a dedicated AfCFTA support mechanism for SIDS. Moreover, it identifies strategic niches—digital trade, blue economy, regional tourism, and service exports—through which African SIDS can strengthen their contribution to continental value chains. The findings highlight the urgency of a differentiated integration strategy that recognises the specific developmental needs of island economies. Ensuring their meaningful inclusion is not only essential for their resilience and growth but also for the overall equity and credibility of the AfCFTA.