Physical activity among people of all ages has been decreasing at an alarming rate in recent years. Active commuting is recognized as a public health strategy to increase physical activity. The objectives of the study were to determine the habit of active commuting and the associated factors of commute mode choice among university students in the secondary city of Sylhet, Bangladesh. The study was cross-sectional in nature, and information from three hundred and forty-eight students was collected through an online survey using Google Forms. In addition to basic statistical tools, a multiple logistic regression model was applied to identify the factors that were associated with the commuting mode choice of the students. The results have shown that the prevalence of using an active commuting mode is not at a satisfactory level (43%). No remarkable difference in commuting behavior was found between males and females. The “distance between campus and students’ residences” and the “mode of commuting preferred by roommate or classmate” are the most significant factors influencing students’ commuting choices and related actions. In addition, respondents with lower socio-economic conditions have more of a tendency to use active modes of commuting. Weather, time constraints, road safety, and family residence in rural or urban areas all have an impact on choosing an active mode of transportation for attending classes, but none is overly significant. It is recommended to promote the health and financial benefits of active commuting. Necessary facilities should be constructed to increase the level of active commuting, such as additional residential halls near campus and developing a built environment on the campus for walking and cycling for both male and female students.