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The presence of sex-based asymmetry in the behaviours of youths with Autism Spectrum Disorder (ASD) is currently under research scrutiny. ASD is characterised by challenging behaviour (CB) and is often accompanied by anxiety, both of which often exacerbate social interaction difficulties. The present study examined the presence of sex-based asymmetry in the <i>prevalence</i> of CB and anxiety and in the <i>association</i> between CB and anxiety in a sample including 32 male autistic youths (<i>M</i> age = 10.09, SD = 3.83, range = 6–18 yr) and 32 female autistic youths (<i>M</i> age = 10.31, SD = 2.57, range = 6–15 yr) matched for age, IQ, and ASD severity (<i>p</i> > .101). While the prevalence and severity of behavioural characteristics across males and females with ASD were similar (<i>p</i> = .767), representing symmetry, there was asymmetry in the ways that CBs and anxiety were associated with each other across the two sexes. Specifically, there were 3 instances of symmetry (<i>r</i> > .3, <i>p</i> < .05)), but there were also 10 occurrences of sex-based asymmetry (<i>r</i> < .3, <i>p</i> > .05) in the association between five aspects of CB and five anxiety disorders. These findings emphasise the underlying sex-based <i>symmetry</i> in the prevalence of ASD-related behaviours, also highlighting unique sex-based <i>asymmetry</i> in the association between CBs and anxiety in autistic youths.