The suggested overlap between autism spectrum disorder (ASD) and gender dysphoria/incongruence (GD/GI) has been much disputed. This review showed a relationship between ASD traits and GD feelings in the general population and a high prevalence of GD/GI in ASD. Our meta-analyses revealed that the pooled estimate of the prevalence of ASD diagnoses in GD/GI people was 11% (p < 0.001) and the overall effect size of the difference in ASD traits between GD/GI and control people was significant (g = 0.67, p < 0.001). Heterogeneity was high in both meta-analyses. We demonstrated that the chances that there is not a link between ASD and GD/GI are negligible, yet the size of it needs further investigation.