IntroductionThe abrupt transition of the mode of learning due to the COVID-19 pandemic resulted in an increase in complaints of musculoskeletal (MSK) discomfort among students in Higher Education Institutions (HEI). Inadequate physical space and equipment are one major cause of these complaints. Among HEIs, physical therapy (PT) students have sufficient background in managing MSK discomforts. However, this does not prevent them from experiencing pain and discomfort during online classes. This analytical cross-sectional study aims to determine the correlation between ergonomic knowledge and MSK discomfort among first-year to fourth-year PT students.Methods and analysisThe study will use two questionnaires, theErgonomic Knowledge Questionnaire,and theCornell Musculoskeletal Discomfort Questionnaire,that determine the level of ergonomic knowledge and MSK discomfort, respectively. This will be disseminated to 144 students through google forms. Results will then be analysed using Pearson Correlation Test. The study anticipates a correlation between the level of ergonomic knowledge and MSK discomfort among the participants.Ethics and disseminationThe study has been approved by the University of Santo Tomas-College of Rehabilitation Sciences Ethics Review Committee. The participants will receive the results prior to publication in a peer-reviewed scientific journal.Trial registration numberPhilippine Health Research Registry with registry ID PHRR230216-005443.