Recent research suggests that maternal mood entropy, a novel measure of mood dysfunction, is associated with child outcomes. However, the link between maternal mood entropy and children’s structural brain development, and how this association may change across childhood, remains unclear. In a longitudinal study with neuroimaging data collected at ages 4.5, 6, 7.5, and 10.5 years (n = 1,498; n = 674 with neuroimaging), we examined whether maternal mood entropy is associated with children’s hippocampal and amygdala volumes over time. Mothers reported on negative mood symptoms at several assessments between ages 3 months and 4.5 years. We calculated maternal mood levels as the sum of mood symptoms and computed maternal mood entropy by applying Shannon’s entropy to the distributions of mood questionnaire responses. Maternal mood measures were not associated with amygdala volumes; however, mood entropy was directly associated with smaller hippocampal volumes at age 4.5 years and indirectly associated with smaller hippocampal volumes at 10.5 years through rank-order stability over time. These effects were present beyond the effects of socioeconomic status and intracranial volume and were specific to mood entropy, not mood levels. Our findings indicate that patterns of maternal mood are embedded in early childhood brain structure, setting the stage for subsequent neurodevelopment.