Introduction: University students had high risk of unhealthy lifestyle habits such as being sedentary and having poor dietary choices due to higher cost of healthy food and the wide availability of fast food. These may contribute to overweight, obesity and co-morbidities. The aim of the study was to determine the association of food choices motives, physical activity (PA) level and body mass index status among undergraduates in Universiti Sains Malaysia. Methods: A total of 125 undergraduate students were recruited. Self-reported online questionnaire was administered to obtain information about sociodemographic information, anthropometric measurements, food choice motives using Food Choices Questionnaire and physical activity using the Global Physical Activity Questionnaire. The association between food choice motive, PA and body mass index was assessed using Spearman correlation and Fisher`s Exact Test. Results: The three most important food choice motives are religion, price and sensory appeal. A total of 16% of the subjects were underweight, 19.2% were overweight and 11.2% were obese. 21.6% of the students had low PA level. There was significant inverse association between sensory appeal and BMI (p = 0.002, r = - 0.269). Physical activity was not significantly different between BMI categories. Conclusion: Those who have lower BMI reported to have greater sensory appeal, but association between PA and body mass index had no significant difference. Future studies are required for understanding the direct impact of food choice motives on dietary quality and its association with PA motivation and BMI status for reducing the prevalence of obesity among undergraduates.