Socioeconomic factors have been consistently linked with the structure of children’s hippocampus and anterior cingulate cortex (ACC). Chronic stress—as indexed by hair cortisol concentration—may represent an important mechanism underlying these associations. Here, the article's authors examined associations between hair cortisol and children’s hippocampal and ACC structure, including across hippocampal subfields, and whether hair cortisol mediated associations between socioeconomic background (family income-to-needs ratio, parental education) and the structure of these brain regions. Participants were 5- to 9-year-old children (N = 94; 61% female) from socioeconomically diverse families. Parents and children provided hair samples that were assayed for cortisol. High-resolution, T1-weighted magnetic resonance imaging scans were acquired, and FreeSurfer 6.0 was used to compute hippocampal volume and rostral and caudal ACC thickness and surface area (n = 37 with both child hair cortisol and magnetic resonance imaging data; n = 41 with both parent hair cortisol and magnetic resonance imaging data). Higher hair cortisol concentration was significantly associated with smaller CA3 and dentate gyrus hippocampal subfield volumes but not with CA1 or subiculum volume. Higher hair cortisol was also associated with greater caudal ACC thickness. Hair cortisol significantly mediated associations between parental education level and CA3 and dentate gyrus volumes; lower parental education level was associated with higher hair cortisol, which in turn was associated with smaller volume in these subfields. These findings point to chronic physiologic stress as a potential mechanism through which lower parental education level leads to reduced hippocampal volume. Hair cortisol concentration may be an informative biomarker leading to more effective prevention and intervention strategies aimed at childhood socioeconomic disadvantage.