Sexuality- and gender-diverse (SGD) young people experience substantial health disparities relative to cisgender heterosexual peers. Little is known about SGD adolescents younger than 15 years. To describe SGD prevalence and associated factors in a population-representative cohort of younger adolescents in Australia. This prospective cohort study was part of the Future Proofing Study, with enrollment of year 8 students at 134 Australian secondary schools from 2019 to 2021 and annual follow-ups for 5 years. Data were analyzed from June 20, 2023, to June 6, 2024. Outcomes of interest were baseline self-reported gender and sexuality identities, individual characteristics, and mental health and disability diagnoses, as well as school characteristics. Among 6388 participants, median (IQR) age was 13.9 (13.6-15.8), with a range of 10.7 to 17.5 years. Most participants attended school in a major city (76.0%), were born in Australia (91.4%), and spoke English at home (93.7%). Approximately half (3122 participants; 48.9% [95% CI, 45.2%-59.0%]) identified as female or girls, and 46.5% (2973 participants; 95% CI, 39.8%-53.4%) identified as male or boys. The overall proportion of transgender identity was 3.3% (95% CI, 2.7%-3.9%), with 23 participants (0.4%) identifying as transgender boys, 10 participants (0.2%) identifying as transgender girls, 117 participants (1.8%) identifying as transgender nonbinary, and 59 participants (0.9%) identifying as another transgender identity. The overall proportion of sexuality diversity was 12.0% (95% CI, 10.4%-13.8%). The proportion of cisgender participants who were sexuality-diverse (13.0% [95% CI, 11.4%-14.8%] of girls and 4.7% [95% CI, 3.7%-5.9%] of boys) was lower than the proportion among gender-diverse participants, which ranged from 30.0% (95% CI, 9.3%-64.1%) of transgender girls to 91.5% (95% CI, 81.3%-96.4%) of those with another diverse gender identity. Gender diversity and sexuality diversity were strongly associated (odds ratio [OR], 66.24; 95% CI, 38.23-114.80), and both were negatively associated with age (gender diversity: OR per 1-year older, 0.61; 95% CI, 0.49-0.76; sexuality diversity: OR per 1-year older, 0.78; 95% CI, 0.65-0.93) and positively with mental health diagnosis (gender diversity: OR, 2.41; 95% CI, 1.79-3.24; sexuality diversity: OR, 2.50; 95% CI, 2.10-2.98), and disability diagnosis (gender diversity: OR, 2.39; 95% CI, 1.68-3.40; sexuality diversity: OR, 1.96; 95% CI, 1.64-2.36). While there were significant associations between individual and school characteristics and responses to gender and sexuality identity items, patterns of association differed, with no consistent association with economic disadvantage. This cohort study of young adolescents found higher rates of SGD than among samples of older adolescents. The significant associations with younger age, poorer mental health, and disability underscored the urgent need for inclusive programs to promote a safe and welcoming environment in schools, health care settings, and communities.