Students with chronic medical conditions often experience barriers to academic progress, including impact of disease and treatment, increased school absence, and altered expectations of teachers and parents. School belonging is an important element of academic success and can be promoted by positive relationships, structure, and support in the school environment. One aim of this study was to explore group differences in perceived school belonging and rate of on-time high school completion for students with chronic medical conditions as compared to their healthy peers. The second goal was to analyze relations between belonging, health status, and on-time completion of high school. Restricted data from Add Health was used to answer the study questions. Results showed that students with chronic medical conditions reported lower levels of perceived school belonging than their healthy peers (t[subscript (1056)] = 3.69, p < 0.001, d = 0.23). Students with chronic medical conditions also attained lower levels of on-time high school graduation than their healthy peers (t[subscript (1056)] = 2.60, p = 0.005, d = 0.16). Perceived school belonging had a different impact for students with chronic medical conditions than for those who had no health concerns. Each unit increase in belonging for students with health impairment was related to a 63% increased likelihood of on-time high school graduation (OR = 1.629, p = 0.003). School belonging is especially important for students living with chronic medical conditions. Finding ways to facilitate a stronger sense of school belonging may be a way to support desired academic outcomes.