Emotional maltreatment is a common form of child abuse with a powerful negative impact on mental health. The aim of this study was to examine the effect of emotional maltreatment on mental health and mental well-being in a general population of Swedish 12- to 13-year old girls and boys. Data was collected via self-report questionnaires in classroom settings from 1134 students. Emotional maltreatment had significant effects on mental health and mental well-being for both girls and boys. Moreover, there were significant interaction effects between gender and levels of emotional maltreatment. Girls reported decreased mental health and mental well-being at lower degrees of emotional maltreatment compared to boys. Furthermore, girls reported larger decreases in mental health in response to exposure of emotional maltreatment. For internalizing symptoms, mental well-being and psychosomatic symptoms, exposure level of emotional maltreatment seemed to magnify the gender differences. For externalizing symptoms, there were no differences between girls and boys in the group reporting no emotional maltreatment and the increase in externalizing symptoms were of equal magnitude for both genders. Given the impact of emotional maltreatment on mental health in the general population, results from this study implies that a trauma-informed perspective is necessary in understanding gender differences in mental health in early adolescence. Further research is needed in order to understand the underlying processes generating the differences in girls and boys responses to emotional maltreatment.