This research focused on assessing the relationship between seaport efficiency and Nigeria’s non-oil export. The western ports of Lagos were selected as the Decision-Making Units (DMU) for this study covering the period of 2000 to 2020. Two stage estimation process was employed. Data Envelopment Analysis (DEA) was deployed in the first stage to generate the efficiency index required to test the relationships. In the second stage, the efficiency index so generated was introduced as one of the independent variables in a multiple regression model, using Autoregressive Distributed Lag Model (ARDL). The finding shows that seaport efficiency has a positive and significant relationship with non-oil export in the long run and a positive but insignificant relationship with non-oil export in the short run. The study concluded that seaport efficiency has a direct and positive impact on Nigeria’s non-oil export. This study therefore recommended the effective implementation of reforms of critical infrastructure particularly the transportation sector for improved efficiency by the federal and state governments; the deepening and close monitoring of the concessionaires by the Nigerian Ports Authority, to meet their investment and operational expectation in the concession agreement.