Background: Despite the recent increase in HIV infections among adolescents, little is known about their HIV knowledge and perceptions. This study, therefore, sought to examine the factors associated with comprehensive HIV knowledge, stigma, and HIV risk perceptions among young adolescents aged 10-14 years in Akwa Ibom State, Nigeria. Additionally, consenting parents and assenting young adolescents were tested for HIV. Methods: We used cross-sectional data from the 2017 Akwa Ibom AIDS Indicator Survey to analyze comprehensive HIV knowledge, stigma, and HIV risk perceptions among young adolescents. Demographic characteristics of young adolescents were summarized using descriptive statistics. Chi-square test (or Fisher's exact test in cases of small subgroup sample sizes) was used to elicit associations between demographics and study outcomes. Separate multivariable logistic regression models were then conducted to determine associations with the study outcomes. Sampling weights were calculated in order to adjust for the sample design. P-values less than 0.05 were considered to be significant. Results: A total of 1818 young adolescents were interviewed. The survey highlighted significant low levels of comprehensive HIV knowledge (9.4%) among young adolescents. Adolescent-parent discussions [AOR = 2.19, 95% C.I (1.10-4.38), p = 0.03], schools as sources of HIV information [AOR = 8.06, 95% C.I (1.70-38.33), p < 0.001], and sexual activeness [AOR = 2.55, 95% C.I (1.16-5.60), p = 0.02] were associated with comprehensive HIV knowledge. Majority (93%) of young adolescents perceived themselves not to be at risk of HIV. Overall, 81.5% of young adolescents reported stigmatizing tendencies towards people living with HIV. HIV prevalence among young adolescents was 0.6%. Conclusions: Results indicate low comprehensive HIV knowledge among young adolescents. Our findings suggest that there is a need for increased attention towards young adolescents particularly in the provision of comprehensive, functional sexuality education, including HIV at the family-and school-levels. Consequently, age appropriate interventions are needed to address the epidemiological risks of young adolescents that are influenced by a myriad of social issues.