Physical exercise helps maintain the overall mental and physical health of a student. However, activity preferences differ in each one of the students. Thus, it affects the willingness and the desire of every student to do physical activities that are different from their choice. Using descriptive – correlational and comparative design, the study aimed to determine the relationship between the level of motivation to exercise and the activity preferences of the students of one of the Catholic schools in Davao City, Philippines. The respondents of the study were the Junior High School (JHS) students who voluntarily participate in the conduct of the study and are chosen randomly using random sampling technique. More particularly, this study sought to determine the level of intrinsic and extrinsic motivation of the students in doing physical exercises and the corresponding indicators of their activity preferences. An adapted and validated-researcher-made questionnaire determined students’ level of motivation and their activity preferences. Findings revealed that there is a correlation between the level of motivation to exercise and the activity preferences of the students since the p-value is greater than 0.05 but is described as a weak positive correlation. Furthermore, Pearson r analysis revealed that the level of motivation has a significant influence to the activity preferences of the JHS students.