Learning Management System (LMS) is an accommodating technology to instructors wherein lessons, quizzes, and other usable features in teaching can be conducted online. There is an LMS used in an engineering institution which won many awards for continuous improvement for the past few years. Yet, students are having difficulties in using the system which can affect their academic performances. In order to certify that there is a problem regarding the usability of the system, an initial data gathering of SUS Questionnaire was conducted to the 100 participating students. The said LMS requires improvement based on the SUS score of 51.75 which is below the marginal average scale of 68. On the other hand, the data of SUS Questionnaire, QUIS, checklist of tasks, and SEQ gathered from 425 students were used for Structural Equation Modelling (SEM) – path analysis to determine the factors affecting the usability of the LMS. The results are the following: (1) effectiveness – usability, (2) screen – usability, (3) task level – usability, (4) terminology – usability, (5) learning – usability, (6) system capabilities – usability, and (7) efficiency – effectiveness. Hence, this research modifies the user interface to increase the usability, and user satisfaction of the said LMS.