Purpose: The primary aim of this study is to evaluate and compare the operational performance of two major seaports in Lagos, Nigeria – Apapa Port and Tin Can Island Port – using specific port performance indicators. Methodology: The study employs the Cobb-Douglas production function and the Ordinary Least Squares (OLS) method to analyse data sourced from the Nigeria Ports Authority's operational bulletin records. The analysis was conducted using E-view software version 10.0. Results: The findings indicate that cargo throughput, used as the dependent variable, has a strong positive linear relationship with ship traffic, berth occupancy, turnaround time, and the number of employees. The R2 value is 85.89% for Apapa Port and 98.79% for Tin Can Island Port, suggesting that Tin Can Island Port is more productive. Theoretical Contribution: This study contributes to the field of maritime transport and logistics by providing empirical evidence on the efficiency and productivity of Nigerian seaports. It highlights the importance of modern infrastructure and effective port operations in enhancing seaport performance. Practical Implications: The study recommends that the Nigerian government should focus on reducing port congestion, improving road conditions leading to the ports, and streamlining port documentation processes. These measures are essential for enhancing the operational efficiency of Nigerian seaports.