Background Prevalence of substance use disorders (SUD) is high among adolescents and young adults (AYAs) with complex medical needs. Little is known about risk factors for SUD in this population. Methods This retrospective cohort study used electronic health record data from a large academic hospital system (2015–2019) to identify adolescents (aged 10–17) and young adults (aged 18–27) with intellectual/developmental disorders, psychiatric conditions, or complex medical conditions. Logistic regression was used to identify demographic, clinical, and neighborhood-level risk factors associated with SUD in this population. Results A total of 149 adolescents and 536 young adults had a SUD diagnosis (6.7% and 20.6%, respectively). Among adolescents, notable risk factors for SUD included age (adjusted odds ratio [aOR] = 1.42, 95% confidence interval [CI] = [1.31, 1.54]), Hispanic ethnicity (aOR = 2.10, 95% CI = [1.10, 3.99]), additional psychoactive medication classes (aOR = 1.27, 95% CI = [1.11, 1.46]), and living in a “high” child opportunity index (COI) (aOR = 2.06, 95% CI [1.02, 4.14]) or a “very high” COI (aOR = 3.04, 95% CI [1.56,5.95]) area. Among young adults, notable risk factors included being male (aOR = 2.41, 95% CI [1.91, 3.05]), being Black (aOR = 1.64, 95% CI [1.28, 2.09]), and additional non-psychoactive (aOR = 1.07, 95% CI [1.03, 1.11]) or psychoactive medication classes (aOR = 1.17, 95% CI [1.07, 1.28]). Limitations These descriptive analyses are limited to one large academic hospital system in North Carolina and may not be representative of all high-need AYAs in the state. Conclusions Several demographic, clinical, and neighborhood risk factors are associated with SUD in high-need AYAs.