Increased food selectivity among children with autism spectrum disorder may lead to nutritional inadequacy. We designed this study to examine the prospective relationship between autistic traits in children and subsequent nutrient intake in later childhood and whether this relationship changes over time. We utilized longitudinal data obtained at two time points from the Shika study, an ongoing population-based study conducted in a rural area of Japan. Participants were 759 Japanese children aged between 7 and 12 years at baseline and between 10 and 15 years in the follow-up. The results obtained showed relatively lower intakes of sodium, calcium, magnesium, iron, vitamin D, vitamin B2, and vitamin B12 among children with than without autistic traits. Interactions were observed among autistic traits and time points for iron, vitamin B2, folic acid, and pantothenic acid. The results of this study suggest the importance of screening the nutrient intake of children with autistic traits across childhood in order to reduce the risk of restricted intake.