School climate is an essential ingredient of student well-being and academic success. Although it has been studied extensively, only a few well-validated instruments are available for the assessment of school climate. The aim of this study was to assess the factor validity and measurement invariance of the Socio-educational Environment Questionnaire (SEQ) using data from a longitudinal cohort of 1036 French-Canadian high school students who were assessed on three occasions. Exploratory structural equation modeling was used to empirically test the factor structure and measurement invariance across time and gender. The results supported the proposed SEQ five-factor model (teacher-student relationship, student relationships, justice climate, academic climate, and safety climate) and its longitudinal invariance across high school years. Gender invariance was also established. Finally, predictive validity was assessed. Among the five school climate dimensions, teacher-student relationships, academic and safety climate were related to subsequent school engagement. School climate was not associated with either boys' or girls' academic achievement. Overall, this study suggests that the SEQ is a valid and reliable short tool for the assessment of school climate in high school.