This study explores whether the interplay of health problems and school environment predicts academic failure, an individual event with consequences for the life course, as well as for society at large. This exploration proceeds in three steps: 1) we examine whether physical and mental health problems are an academic risk factor during secondary school; 2) we investigate the academic mechanisms underlying this risk status; and 3) we explore whether this risk status varies by school context. A series of logistic regressions reveals that self-rated health and emotional distress are both associated with greater likelihood of failing one or more classes in the next year and that absenteeism, trouble with homework, and student-teacher bonding account for much of these associations. Associations of physical and mental health problems with academic failure vary only slightly across schools, however. We discuss the implications of these findings for both research and policy and argue that the examination of overlap among different domains of adolescent functioning can advance the sociological understanding of health, education, and social problems in general.