Background Previous research has suggested that overweight children have a higher risk of behavior problems, but the causal direction of this relationship remains unclear. In a large prospective population study, we investigated whether child behavior problems and body mass index are associated in toddlers and whether overweight is a risk for behavior problems or vice versa. Methods The study was part of the Norwegian Mother and Child Cohort Study. The sample consisted of 10 860 toddlers, followed up to age 36 months. We used data from maternal questionnaires from gestation week 17 and at child ages 18 and 36 months, and data from the Medical Birth Registry of Norway. Child height and weight were assessed at child health stations and recorded by mothers. Behavior problems were assessed using shortened subscales from the Child Behavior Checklist. Statistical analyses were conducted using structural equation modeling. Results Behavior problems in toddlers were not associated with higher body mass index cross-sectionally at either age 18 or 36 months, and there was no indication that behavior problems caused increasing body mass index over time or vice versa. Conclusions The association between behavior problems and body mass index found in older children did not appear in toddlers up to age 36 months. Future studies should focus on the age span from 3 to 6 years, which includes the period of adiposity rebound.