Previous studies carryout revealed that many factors influence container terminal efficiency. This study revealed that factors such as inadequate quay/gantry crane equipment, reducing berth times and delays of container ships, dwell time, container cargo and truck turnaround time, custom clearance, limited storage capacity, poor multi-modal connections to hinterland and infrastructure directly influencing container terminal efficiency. The research document thoroughly explored these factors and discussed the extent to which they influence container terminal efficiency within the port industry. The primary objective of this study was to assess factors influencing Container Terminals Efficiency with a case study of the Mombasa Entry Port. The target population of the study was approximately 500 people which included Kenya Port Authority, Conventional Cargo Operations, and Container Terminal Operations. Questionnaire was the major instrument used to obtain primary data from the respondents; while the secondary data were obtained from existing empirical literature relevant to the study. The study employed an exploratory approach using a descriptive survey design. The questionnaire be designed using Likert scale type. A sample of 50 respondents was obtained through a stratified sampling technique of which 30 of the respondents participated in the survey. Data were analyzed using the Statistical Package for Social Sciences (SPSS) and Microsoft Excel 2013. The findings revealed 86.7% of the respondents believe that by improving the infrastructures at the port of Mombasa will minimize the congestion problems that sometime occur. Findings from the survey revealed that 83.3% of the respondents agree that the lack of Integrated IT system poses substantial delays in custom clearance procedures. The study also recommended that Kenya Port Authority (KPA) continuously invest in modern quay and gantry cranes to supplement the current ones in order to continuously enhance productivity of port operations and that the Government of Kenya invest in expanding the physical infrastructure such as adequate berthing facilities, wharves, yard capacity, quayside, railway, as well as hinterland connections expansion.