The ability of an airport to attract traffic can vary within a multi-airport model of operation and highly competitive environment. This study is an effort to examine the factors that cargo agents rank as most important in their choice of Abuja airport cargo transhipment operations. A questionnaire survey was conducted on a random sample of members of the Association of Nigeria Customs Licensed Agents (ANCLA) at Abuja airport for primary data collection. The study employed a combination of Factor Analysis (FA) and Multiple Linear Regression (MLR) to analyse the data collected. The results of the factor loadings indicate airport capacity, airport charges and customs efficiency as the most significant factors that agents consider in their choice of handling cargo through Abuja airport. The three variables were found to have a high correlation relationship (R = 0.802) with the dependent variable of airport choice after subjecting it to regression analysis. This serves as information to airport managers for the airport planning of capacity in cargo operations within multi-airport country such as Nigeria.