Age at autism diagnosis is associated with sex assigned at birth (hereafter, "sex"), such that girls/women are more likely to be delayed or "missed" entirely in the diagnostic process compared to boys/men. Later diagnosed individuals, especially girls/women, demonstrate increased anxious/depressive symptoms. Data on autistic youth from clinic-based (n = 1035; 22.9% assigned female) and sex-balanced research-based (n = 128; 43% assigned female) samples were probed via regression-based mediation models to understand relationships between diagnostic age, sex, and symptoms of anxiety/depression. We hypothesized diagnostic age would mediate the relationship between sex and anxious/depressive symptoms. In both samples, later diagnostic age predicted greater anxious and depressive symptoms, and sex did not directly predict anxious symptoms. In the clinic-based but not the research-based sample, individuals assigned female at birth were later diagnosed than those assigned male, and there was a significant indirect effect of sex on anxious and depressive symptoms through diagnostic age, such that those assigned female and later diagnosed experienced greater symptoms. Within the research-based sample only, sex predicted depressive symptoms. The present study provides an important impetus for further evaluating the implications of diagnostic timing, enhancing tools for recognizing autism in individuals assigned female at birth, and grounding research with real-world ascertainment strategies.