Abstract: The paper aims to examine the factors that affects the successful implementation of the Mastery-based Individualized Learning Enhancement System (MILES) in the Far Eastern University (FEU) Institute of Technology. Two periods were analyzed which are the initial implementation, and this is the start of the pandemic period, and the year after the initial implementation of MILES. The Artificial Neural Network (ANN)-Particle Swarm Optimization (PSO)-based Sensitivity Analysis (SA) was utilized to determine the relative importance (RI) index among the influencing factors that affects the students’ level of satisfaction of the MILES implementation. Survey questionnaires were deployed through the canvas platforms and were answered by the students. In the initial survey, a total of 5763 students responded. For the SY 2020-2021, it was observed that the most influential variable to the student’s performance during the MILES Implementation is Course Adviser Rating while the parameters with the least impact to the student’s performance is the Student’s Status as regular or irregular student. For the survey on SY 2021-2022, the highest relative index is for the lesson preference while the lowest importance index is for the opportunities. Findings of the study shows that the use of NN-PSO based sensitivity analysis is an effective tool for establishing the significance of each variable to a target output.