Studies show that adolescents have a heightened sensitivity to the urban context, such as violence. This study explores factors influencing and determine the areas of influence of students’ perceived stress when commuting from home to school in the city of Medellin, Colombia. To achieve these aims, a cross-sectional survey research design was employed with students in one school. A total of 301 students (aged 14–18) were chosen using convenience sampling. The data were analyzed using Machine Learning methodology (ML). Furthermore, a Geographic Information System (GIS) was employed to create an isoprobability map of areas of perceived stress. Among the students interviewed, 22.7% experienced stress while traveling to school. Socioeconomic, accessibility, transport and safety, urban violence and quality of life categories were found to be associated with school commute-related perceived stress. Within these categories, the traditional variables of distance (odds ratio [OR] = 5.21) and mode of travel (OR = 11.05) are significant. In addition, socioeconomic status (OR = 4.49), urban violence (OR = 1.04), high traffic accidents on the route to school (OR = 21.83) and poor perceived health (OR = 9.10) are significant and have a strong effect on stress. Stress perceived by adolescents during school commutes is largely explained by variables related to social and environmental factors that do not depend on the individual, such as urban violence, traffic accidents or the state of sidewalks. Therefore, public authorities should take appropriate measures to reduce students’ stress during school commutes, which would have a positive effect on these adolescents. © The Author(s) 2024.