Data envelopment analysis (DEA) is used to assess the efficiency of 15 container terminals in Africa. The models proposed by Charnes, Cooper and Rhodes (1978) and Banker, Charnes and Cooper (1984) are used to determine and rank the efficiencies of the container terminals for 2013 and 2014. The results show that selected South African container terminals can improve on their operations relative to some of their neighbours to the North. Bootstrapping methods are used to investigate and clarify the results. The Malmquist Productivity Index (MPI) model is used to track and explain changes in efficiency over the period of assessment.