Educational institutions implemented changes in the learning setup due to the COVID-19 pandemic. While some universities returned to in-person classes, some adopted hybrid setups. This study investigates the 3rd year Industrial Engineering student’s perceived workload, stress, and fatigue throughout a semester in a blended learning mode, transitioning from a fully remote setup. Student experiences were correlated with their mental health and academic performance. Sixty-six participants completed the 20-week study during the 2nd semester of AY 2022–2023. Results show that students’ workload, stress, fatigue, and mental health differed significantly over time. The outcomes were not statistically different between males and females. Depression and anxiety were related to students’ perceived stress and fatigue, stress was related to the students’ perceived workload and fatigue, and the perceived academic performance was related to the perceived workload, stress, and fatigue. Recommendations for further studies include expanding the study to a wider population, increasing the sample size, and examining the implications of having breaks during the semester.