Cross-sectional research has demonstrated the overrepresentation of gender dysphoria in children and adults with autism spectrum disorder. However, the predictors and underlying mechanisms of this co-occurrence remain unclear. This follow-up study aimed to explore baseline (childhood/adolescence) predictors for the follow-up (adulthood) self-reported wish to be of the opposite sex and to investigate its mental health correlates in a sample of 88 autistic individuals as compared with 42 typically developing controls. An item on the Adult Self-Report Inventory-4, "I wish I was the opposite sex," was used. We compared mental health symptoms between adults with and without this item endorsement. We used prediction models to explore family and autism-related predictors in childhood/adolescence to endorse this item in adulthood. There were more adults endorsing the item in the autism spectrum disorder group compared with the typically developing group. Autistic adults who endorsed the item experienced more mental health challenges, more bullying victimization, more suicidal ideations, and worse quality of life. Lower parent-reported family support and more stereotyped/repetitive behaviors during childhood/adolescence predicted the self-reported wish to be of the opposite sex in adulthood in autistic individuals. It is necessary to raise more attention to gender development and related mental health impact in autistic individuals.