Small-scale aquaculture in Malawi is thought to contribute to nutrition and food security and serve as an income diversification strategy. Nevertheless, its adoption is low. Drawing on a recent survey of 734 small-scale fish farms across the country, the present study assesses the productivity and profitability of small-scale fish farms, and their determinants using regression analysis. Most fish farms are owned and managed by individual farm-households, though communally owned farms are also present. Small-scale aquaculture is found to be profitable, though the gross margins are slim. Regression results reveal that productivity and profitability are positively affected by the use of farms for both fingerling and grow-out production; the use of high-quality inputs such as commercial feed and inorganic fertilizers; and number of years the farm has existed. These results confirm that small-scale fish farmers in Malawi and other similar settings should adopt improved technologies and practice best on-farm management practices to increase productivity and profitability. This study contributes to the discourse regarding the pathway through which aquaculture in Malawi can achieve its potential to contribute to the country’s development.