Globally, depression and anxiety are major public health concerns with onset during adolescence. While rural Australia experiences overall lower health outcomes, variation in mental health prevalence rates between rural and urban Australia is unclear. The aim of this paper was to estimate the pooled prevalence rates for depression and anxiety among young Australians aged between 10 and 24 years. Selected studies from a systematic literature search were assessed for risk of bias. Random effects model using DerSimonian and Laird method with Freeman–Tukey Double Arcsine Transformation was fitted. Sensitivity analyses were performed. Prevalence estimates were stratified by region and disorder. The overall pooled prevalence of depression and anxiety was 25.3% (95% CI, 19.9–31.0%). In subgroup analysis, anxiety prevalence was 29.9% (95% CI, 21.6–39.0%); depression: 21.3% (95% CI, 14.9–28.5%); and depression or anxiety: 27.2% (95% CI, 20.3–34.6%). Depression and anxiety prevalence were higher in urban 26.1% (95% CI, 17.3–35.9%) compared to rural areas 24.9% (95% CI, 17.5–33%), although the difference was not statistically significant. The heterogeneity was high with an I2 score of 95.8%. There is need for further research on healthcare access, mental health literacy and help-seeking attitude in Australia.