Gender variance (GV) and autism spectrum disorder (ASD) frequently co-occur in clinical populations. We investigated GV in association with ASD characteristics in nonclinical children and in children with developmental/mental health diagnoses. In 6–12-year-olds (N = 2445; 51% birth-assigned boys), the Gender Identity Questionnaire for Children measured GV and the Children’s Social Behavior Questionnaire measured six subdomains of ASD characteristics. Among nonclinical children, GV was associated with parent-reported difficulties orienting socially and stereotyped behaviors. GV was also associated with parent-reported clinical diagnoses of ASD, sensory processing disorder, and oppositional defiant disorder. These findings suggest associations between specific ASD characteristics and GV in nonclinical children. Also, childhood GV should be further examined in a range of clinical populations, including ASD individuals.