Studies show that adolescent girls who experience violence grow up with fear and develop survival mechanisms that increase their susceptibility to sexually transmitted infections including HIV. However, the relationship between violence and the development of sexual behavior in young adolescent girls is under-investigated. We examined the Malawi Schooling and Adolescent Study data to explore the associations between home- and school-based violence and sexual behaviors in 416 young adolescent girls in rural Southern Malawi. Bivariate Logistic Regression analysis was applied to determine associations. Of 353 (84.9%) girls who had sex with a male partner, 123 (34.8%) experienced home-based violence, and 53 (15%) experienced school-based violence. The odds of girls who experienced home-based violence (OR = 2.46, 95% CI = 1.21, 5.01) and those who first experienced home-based violence between 13 and 14 years (OR = 2.78, 95% CI = 1.35, 5.74) were higher among girls who had multiple sexual partners than those with a single sexual partner. With school-based violence, sexual initiation, having multiple sexual partners, and not using protection were positively associated with experiencing teasing, sexual comments, punching, and touching in private areas in transit to school and by a teacher. These results suggest that home- and school-based violence should be essential components of research and biobehavioral interventions targeting the sexual behaviors of young adolescent girls.