We investigated how gender identity, sexual orientation, and race/ethnicity intersect to shape the social epidemiology of HPV vaccination initiation among U.S. college students. Cross-sectional survey data were from the National College Health Assessment (Fall, 2019-Spring, 2020; N = 65,047). We conducted an intersectional Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy by nesting participants within 36 social strata defined using gender identity, sexual orientation, and race/ethnicity. Bayesian multilevel logistic regression models with random intercepts for social strata were fit for HPV vaccination initiation. Intersectional models adjusted for the additive main effects to isolate intersectional interactions, controlling for age and geographic region. Social strata that included cisgender men, transgender women, and non-binary assigned-male-at-birth individuals and strata that included racial/ethnic minorities had a significantly lower likelihood of HPV vaccination initiation relative to strata including cisgender women and non-Hispanic White individuals, respectively, while strata including lesbian/gay and bisexual/pansexual/queer individuals had a significantly higher likelihood of HPV vaccination initiation relative to strata including heterosexual individuals. We also observed substantial between-stratum inequities in the predicted prevalence of HPV vaccination initiation, with estimates ranging from 59.2% for heterosexual, racial/ethnic minority, cisgender men to 87.1% for bisexual/pansexual/queer, racial/ethnic minority, non-binary assigned-female-at-birth individuals. That being said, the majority of the observed between-stratum variance was driven by additive rather than intersectional interaction effects and the discriminatory accuracy of intersectional stratification with respect to predicting HPV vaccination initiation was low. Collectively, our findings point to a need for more universal guidelines and clinician recommendations that promote HPV vaccine uptake for all adolescents, regardless of race/ethnicity, gender identity, sex-assigned-at-birth, or sexual orientation; however, utilizing an intersectional lens will ensure that resulting public health interventions address inequities and center the needs and experiences of multiply marginalized adolescents.