Bullying and substance use represent serious public health issues facing adolescents in the United States. Few large-sample national studies have examined differences in these indicators by gender identity. The Teen Health and Technology Study (N = 5,542) sampled adolescents ages 13 to 18 years old online. Weighted multivariable logistic regression models investigated disparities in substance use and tested a gender minority social stress hypothesis, comparing gender minority youth (i.e., who are transgender/gender nonconforming and have a gender different from their sex assigned at birth) and cisgender (i.e., whose gender identity or expression matches theirs assigned at birth). Overall, 11.5% of youth self-identified as gender minority. Gender minority youth had increased odds of past-12-month alcohol use, marijuana use, and nonmarijuana illicit drug use. Gender minority youth disproportionately experienced bullying and harassment in the past 12 months, and this victimization was associated with increased odds of all substance use indicators. Bullying mediated the elevated odds of substance use for gender minority youth compared to cisgender adolescents. Findings support the use of gender minority stress perspectives in designing early interventions aimed at addressing the negative health sequelae of bullying and harassment.