Background <p>Adolescent primary hypertension is associated with decreased neurocognitive performance, a finding suggestive of early target organ damage to the brain. We aimed to determine if adolescent hypertension is associated with altered brain magnetic resonance imaging metrics when compared to normotensive controls.</p> Methods <p>Fifty-four newly diagnosed hypertensive subjects and 54 matched controls (age 13–18&#xa0;years) were studied. All participants had neurocognitive testing and brain MRI to measure cortical thickness and gray matter volume, as well as diffusion metrics to determine white matter microstructural integrity.</p> Results <p>The hypertension and control groups showed no significant differences with respect to age, sex, maternal education, income, race, ethnicity, obesity, or laboratory evaluation. While both groups experienced high neighborhood disadvantage, control subjects had higher disadvantage scores (<i>p</i> = 0.03). Adjusted analyses revealed that subjects with hypertension performed similarly to controls on direct neurocognitive testing but received worse parent ratings of executive function. Multivariate analyses found no association between hypertension and brain MRI metrics. However, high neighborhood disadvantage correlated with significantly reduced gray matter volume, and increased BMI <i>z</i>-scores were linked to changes in white matter diffusion metrics but not cortical thickness or gray matter volume.</p> Conclusions <p>Adolescent hypertension itself was not directly linked to changes in brain MRI metrics. High neighborhood disadvantage and obesity, both common in adolescents with primary hypertension, were independently associated with altered gray matter volume and white matter microstructure, respectively.</p> Graphical Abstract <p></p>