Background: During the COVID-19 pandemic, the world found it necessary to adapt its activities to reduce the risk of contagion, so many schools took their classes online, having the freedom to choose their position and place to take the classes. Objective: To determine the factors associated with musculoskeletal pain in university students during the online class stage. Methods: a cross-sectional, prospective, observational, analytical study was carried out. University students from Veracruz, Mexico, between the ages of 18 and 35, who were in online classes, were included. Those who did not agree to participate were excluded. The main variables were the place where you take the class, the hours you spend sitting per day, the physical activity you practice, the presence of muscle pain and its characteristics. Results: 1284 students from the main universities of the place participated, 60% indicated having some muscle pain, mainly in the lower back (47%) and neck (46.8%); 37% of the students with pain tried to correct their posture, 15.3% went to the doctor and and 47.7% tried to solve the pain in an alternative way. The factors associated (OR/CI95%) with the prevention of muscle pain were being male (0.5/0.4-0.6), not working in addition to school (0.7/0.6-0.9), taking classes in a chair with a backrest in front of a table (0.7/0.5-0.9), spending a maximum of 5 to 6 hours sitting (0.7/0.5-0.9), while the risk factors for pain are taking classes sitting in bed (1.5/1.05-2.1), sitting 7 hours or more (1.4/1.1-1.8) and not doing physical activity (1.5/1.2-1.9). Conclusions: Posture, physical activity and sitting hours are determining factors for presenting muscle pain, so education towards university students on postural hygiene and protective factors for pain should be taken into account, in order to reduce the prevalence of this pathology in similar academic situations.