This study used the National Longitudinal Study of Adolescent Health to explore gender differences in the relationship between body perceptions and behavior and changes in adolescents’ psychological well-being over a one-year time period. The sample included 12,814 adolescents (51% girls) aged 11–20 comprised of 68% Non-Hispanic White, 15% African American, 12% Hispanic, and 4% Asian. Perceptions of being larger or more developed generally decreased girls’ psychological well-being over time. Body perceptions and behavior did not significantly influence changes in boys’ psychological well-being over time. Non-Hispanic White girls were the most influenced and Non-Hispanic White boys were the least influenced by body perceptions and behavior. Perceived relative development influenced early adolescent girls, whereas perceptions of being overweight influenced middle to late adolescent girls. Additionally, trying to lose weight influenced middle adolescent boys and girls. These results imply that body perceptions and behavior disadvantage girls’ psychological well-being relative to boys during adolescence.