The present study measured the relative efficiency of five major commercial ports in West Africa, using three different Data Envelopment Analysis (DEA) methods, the CCR, BCC, and Windows I-C methods over the years 2005-2016. Seven input variables and one output variable were used in the model analysis. The CCR and BCC methods were used to evaluate the technical and scale efficiency while the Windows I-C method provided a comprehensive ranking of the studied ports. The results showed that the scale efficiency score of 89.53% indicated that on average the production scale of the ports had deviated from the most productive scale size (MPSS) by 10.47%. These results revealed that the source of the overall inefficiency is due to scale rather than pure technical inefficiency. Hence, in order to improve the overall efficiency, the two scaled inefficient ports of Abidjan and Cotonou should adjust their scale of operations. Then, further investigations were conducted to detect correlations between various variables used in this study. The research found that the absence of any correlation for non-significant variables and negative correlation for the significant variables throughout time resulted from the fact that these variables were not fully utilized. Meaning that they were not efficiently used to boost the container throughput on a scale basis, the research also found that a pandemic or insecurity could easily impact seaports activities with the case of the Ebola outbreak which strucked the West African region from the year 2013 to 2016, or the terrorism threats which prevailed in the region around the year 2012. Thus, for ports to stand out in the present fiercely competitive environment, ports authorities ought to analyze their operational scale to identify whether or not the production size is fitting before further port capacity expansion.