Throughout the COVID-19 pandemic, students face intolerable mental and physical discomfort when taking online classes, directly impacting their learning motivation and academic performance. Related studies indicated that students had negative sentiments regarding online learning. This may be an alarming notion for students, particularly regarding their learning ability and participation in school. To overcome this nuisance, the primary objective of this study was to examine the factors affecting students’ learning motivation and academic performance during online learning using a novel framework of ergonomic appraisal. A total of 316 respondents answered the online questionnaire using a purposive sampling approach through social media platforms. Ergonomic-based indicators for physical, cognitive, and macro-ergonomics were analyzed simultaneously using partial least square structural equation modeling (PLS-SEM). The results showed that the design of the workstation, the use of LMS, access to technology, teaching delivery, temperature level, and visual learning style were found to significantly influence students’ learning motivation, which then impacts the student’s academic performance. Thus, it is essential for those who are facilitating distance learning to keep in mind the factors that could motivate the student. As a result, this paper becomes an avenue to help appropriately plan the course program to ensure its viability and productively engage the students since online learning is becoming increasingly necessary. Further, this article also provides recommendations and implications on assisting schools, educators, and students in aiding a student’s learning motivation and academic performance.