Data envelopment analysis (DEA) has many advantages for analyzing the efficiency of decision-making units, as well as drawbacks, such as a lack of discrimination power. This study applied bi-objective multiple-criteria data envelopment analysis (BiO-MCDEA), a programming approach used to overcome the limitations of traditional DEA models, to analyze the efficiency of 20 Brazilian ports with a consideration of six input and one output variables from 2010 to 2016. Two time-related variables were included to reflect current problems faced by Brazilian ports experiencing long wait times. The results reveal a significant disparity in port efficiency among Brazilian ports. The top five most efficient ports are those with the highest cargo throughput. A clustering analysis also confirmed a strong correlation between cargo throughput and port efficiency scores. Total time of stay, pier length, and courtyard also had strong correlations with the efficiency scores. The clustering method divided Brazilian ports into three groups: efficient ports, medium efficient ports, and inefficient ports.