Lifestyle characteristics can modify the self-rated health of young people, but additional prospective evidence is needed. This study examined the association between changes in lifestyle and self-rated health among students. A secondary analysis of the "Saúde na Boa" project was performed, considering data from 984 students (14-24 years old, 56.9% girls) who were randomly selected from 20 public schools in Recife and Florianopolis, Brazil. Two sets of data 9-months apart were collected, and self-reported data about lifestyle characteristics (physical activity practices, TV watching time, dietary habits, alcohol and tobacco consumption, and sleep time) and self-rated health (poor, fair, good, very good and excellent) were obtained. Differences in self-rated health between collections were categorized as negative changes, stable (no changes) or positive changes. Adjusted multinomial logistic regression analysis was used (p < 0.05). After adjustment for confounding variables, increasing the weekly frequency of active commuting to school (adjusted odds ratio [aOR] = 2.06) and intake of fruits/fruit juice (aOR = 1.81), as well as reducing the monthly frequency of alcohol consumption (aOR = 2.17), was significantly associated with positive changes in self-rated health. Consumption of sweets was also associated with stable self-rated health. In conclusion, our prospective evidence demonstrated that changes in lifestyle characteristics appear to be essential to ensure or generate positive self-rated health in youth.