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Abstract Social isolation during development, especially in adolescence, has detrimental but incompletely understood effects on the brain. This study investigated the neural correlates of preference for solitude and social withdrawal in a sample of 2809 youth [median (IQR) age = 12.0 (1.1) years, 1440 (51.26%) females] from the Adolescent Brain Cognitive Development study. Older youth whose parents had mental health issues more frequently preferred solitude and/or were socially withdrawn (β = 0.04 to 0.14, CI = [0.002, 0.19], P < 0.05), both of which were associated with internalizing and externalizing behaviors, depression, and anxiety (β = 0.25 to 0.45, CI = [0.20, 0.49], P < 0.05). Youth who preferred solitude and/or were socially withdrawn had lower cortical thickness in regions involved in social function (cuneus, insula, anterior cingulate, and superior temporal gyri) and/or mental health (β = −0.09 to −0.02, CI = [−0.14, −0.003], P < 0.05), and higher amygdala, entorhinal cortex, parahippocampal gyrus, and basal ganglia volume (β = 2.62 to 668.10, CI = [0.13, 668.10], P < 0.05). Youth who often preferred solitude had more topologically segregated dorsal attention, temporoparietal, and social networks (β = 0.07 to 0.10, CI = [0.02, 0.14], P ≤ 0.03). Socially withdrawn youth had a less topologically robust and efficient (β = −0.05 to −0.80, CI = [−1.34,−0.01], P < 0.03) and more fragile cerebellum (β = 0.04, CI = [0.01, 0.07], P < 0.05). These findings suggest that social isolation in adolescence may be a risk factor for widespread alterations in brain regions supporting social function and mental health.