Autistic-like features and functional somatic symptoms (FSS) frequently co-occur. It remains unknown how autistic-like features and FSS affect each other and develop throughout adolescence. This study examined reciprocal relations between autistic-like features and FSS in adolescence. Participants were 2772 adolescents (52.5% male) from the Tracking Adolescents’ Individual Lives Survey population and clinical cohort. Data from four waves were included, covering the ages between 11 and 19 years. Autistic-like features were measured using the Children’s Social Behavior Questionnaire. FSS were assessed using the Youth Self Report and Adult Self Report, respectively. Using the random intercept cross-lagged panel model, a stable positive, moderately strong between-persons association was found between autistic-like features and FSS. No within-persons reciprocal effects from wave to wave were observed. Secondary analyses revealed a consistent relation with FSS for three different domains of autistic-like features (social and communication behaviors, repetitive behaviors, and self-regulatory behaviors), and highly similar interrelations in a subsample of adolescents with a clinical autism spectrum disorder diagnosis. In conclusion, the co-occurrence between autistic-like features and FSS is stable throughout adolescence. Clinicians working with adolescents with autistic-like features should be alert to the presence FSS, and vice versa.