Possible mechanisms by which maternal pre-pregnancy body mass index (BMI) programs offspring mental disorders in late childhood are not fully clarified. To assess the association between maternal BMI and mental health problems at 11 years old, we used data from the 2004 Pelotas birth cohort which comprised 4231 newborns. Maternal pre-pregnancy BMI was analyzed as underweight (< 18.5), normal (18.5–24.9), overweight (25.0–29.9), and obesity (≥ 30.0). Mental health problems were assessed at the child’s age of 11 years by the Strengths and Difficulties Questionnaire, total difficulties score and subscale scores (emotional symptoms, conduct problems, hyperactivity/inattention, and peer relationship problems), dichotomized into normal/borderline and abnormal category. The associations between maternal pre-pregnancy BMI and mental health problems in the whole sample and stratified by sex were estimated using crude and adjusted linear and logistic regression. Both linear and logistic regression showed that pre-pregnancy weight was associated with mental problems in early adolescents. Maternal pre-pregnancy obesity was associated with increased odds of total difficulty score among the whole sample. Boys whose mothers were pre-pregnancy overweight had higher odds of conduct problems (OR = 1.56; 95% CI: 1.13, 1.95), when compared to children of normal pre-pregnancy weight mothers, even after adjustments. Maternal pre-pregnancy obesity was associated with mental health problems in early adolescents; specifically, pre-pregnancy overweight increased the risk for conduct problems in 11 years old boys.