Background: Comprehensive neuropsychological testing for adolescents living with HIV is rare and often impractical for overstretched healthcare systems in low-resourced settings. This study aimed to 1) test the potential of a simple algorithm to screen for cognitive and functional difficulties among at-risk adolescents, and 2) using this algorithm, investigate the correlates of cognitive and functional difficulties in a large community-traced sample of South African adolescents. Methods: The study interviewed 10-19-year-old adolescents living with HIV (n = 1059) and uninfected community controls (n = 467), attending 53 public health facilities in the Eastern Cape in 2014-15. Cognitive and functional difficulties were assessed using an algorithm (either adolescent reports of memory, attention or concentration problems, or < 60% total recall on a memory task, or caregiver reports of an adolescent being a ‘slow-learner’, or attending a special needs school) and adolescent reports of functional difficulties. Data on healthcare and psychosocial variables were also collected. Multivariable logistic regressions tested correlates of cognitive and functional difficulties, controlling for sociodemographic and household covariates. Results: Across the sample, the prevalence of cognitive and functional difficulties was 19.3% (95% CI: 17.4-21.4). Adolescents living with HIV had significantly higher rates of cognitive and functional difficulties than community controls (21.9% vs. 13.5%, p<.001). Validating the algorithm with self-reported school grade repetition (lifetime) and number of grades repeated, cognitive and functional difficulties were associated with higher odds of lifetime grade repetition (aOR1.62 95%CI 1.24-2.11) and a higher likelihood of repeating multiple grades (β=0.27, p<.001). Independent of covariates, potential correlates of cognitive and functional difficulties among adolescents were higher depressive symptoms (aOR1.18 95%CI1.11-1.26), concurrent infections (aOR1.92 95%CI1.44-2.58), and more often missing school for clinic appointments (aOR1.66 95%CI1.24-2.23). Conclusions: Cognitive and functional difficulties were more prevalent among adolescents living with HIV than community controls and were associated with psychosocial, physical health, and healthcare factors. Simple algorithms – like the one tested in this study – may be feasible for use in low-resourced settings, following validation against neuropsychological assessment batteries in specialised facilities. Routine screening for cognitive and functional difficulties may be integrated into HIV care to identify adolescents for additional support.