One of the most pressing challenges facing food systems in Africa is ensuring availability of a healthy and sustainable diet to 2.4 billion people by 2050. The continent has struggled with development challenges, particularly chronic food insecurity and pervasive poverty. In Africa’s food systems, fish and other aquatic foods play a multifaceted role in generating income, and providing a critical source of essential micronutrients. To date, there are no estimates of investment and potential returns for domestic fish production in Africa. To contribute to policy debates about the future of fish in Africa, we applied the International Model for Policy Analysis of Agriculture Commodities and Trade (IMPACT) to explore two Pan-African scenarios for fish sector growth: a business-as-usual (BAU) scenario and a high-growth scenario for capture fisheries and aquaculture with accompanying strong gross domestic product growth (HIGH). Post-model analysis was used to estimate employment and aquaculture investment requirements for the sector in Africa. Africa’s fish sector is estimated to support 20.7 million jobs in 2030, and 21.6 million by 2050 under the BAU. Approximately 2.6 people will be employed indirectly along fisheries and aquaculture value chains for every person directly employed in the fish production stage. Under the HIGH scenario, total employment in Africa’s fish food system will reach 58.0 million jobs, representing 2.4% of total projected population in Africa by 2050. Aquaculture production value is estimated to achieve US$ 3.3 billion and US$ 20.4 billion per year under the BAU and HIGH scenarios by 2050, respectively. Farm-gate investment costs for the three key inputs (fish feeds, farm labor, and fish seed) to achieve the aquaculture volumes projected by 2050 are estimated at US$ 1.8 billion per year under the BAU and US$ 11.6 billion per year under the HIGH scenario. Sustained investments are critical to sustain capture fisheries and support aquaculture growth for food system transformation towards healthier diets.