Children with autism spectrum disorder are at risk of developing internalizing and externalizing problems. However, information on early development of behavior problems and the contributing role of emotional functioning in preschool children with autism spectrum disorder is scarce. This study collected data of boys with and without autism spectrum disorder ( N = 156; age: 2–6 years) over three consecutive years (three waves), about their internalizing and externalizing symptoms and emotional functioning (i.e. emotion control, recognition, and vocabulary), using parent-report questionnaires. No age effect was found on internalizing or externalizing problems for boys with and without autism spectrum disorder. Boys with autism spectrum disorder displayed more behavior problems than their typically developing peers and showed lower levels of emotional functioning. Better emotion control and improved emotion recognition were associated with a decrease in problem behaviors for boys with and without autism spectrum disorder, whereas improved emotion vocabulary was uniquely related to a decrease in externalizing problems in boys with autism spectrum disorder. Our findings suggest that boys with and without autism spectrum disorder showed similar developmental courses of internalizing and externalizing problems. However, lower levels of emotional functioning were already more pronounced in boys with autism spectrum disorder at a young age. This contributes to higher levels of behavior problems.