Children with Autism Spectrum Disorder (ASD) often exhibit problematic eating behaviors, an observation mostly based on male dominated, clinical ASD study samples. It is, however, important to evaluate both children with an ASD diagnosis and children with subclinical autistic traits as both often experience difficulties. Moreover, considering the suggestion of a possible girl-specific ASD phenotype, there is a need to determine whether autistic traits are related with problematic eating behaviors in girls as well. This study explores the sex-specific association between autism (both autistic traits and diagnosed ASD) and eating behavior in middle childhood in Generation R, a prospective population-based cohort from fetal life onwards. We collected parental reports of autistic traits at six years (Social Responsiveness Scale) and of eating behavior at ten years (Children's Eating Behaviour Questionnaire). In this cohort of 3559 children, autistic traits at six years were associated with more Picky Eating, Emotional Eating and Food Responsiveness in later childhood (e.g. adjusted B for Picky Eating = 0.07; 95% CI: 0.03, 0.11). Stratified analyses showed that in girls, autistic traits were associated with more Emotional Overeating and Emotional Undereating (e.g. adjusted B for Emotional Undereating = 0.12; 95% CI: 0.04, 0.20), while no associations were found for boys. Results comparing children with and without an ASD diagnosis in the cohort largely confirm these associations (e.g. in girls, adjusted B for Emotional Undereating = 0.72; 95% CI: 0.01, 1.42). Our results point to a sex-specific association between autism and eating behavior in middle childhood. Also, our study is the first study to show that autistic traits are associated with emotionally based eating problems in girls and possibly represent part of a girl-specific ASD phenotype.