Puberty is the defining process of adolescence, and is accompanied by divergent trajectories of behavior and cognition for males and females. Here we examine whether sex differences exist in the effect of puberty on the morphology of the hippocampus and amygdala. T1-weighted structural neuroimaging was performed in a sample of 524 pre- or postpubertal individuals ages 10 to 22 years. Hippocampal and amygdala volume and shape were quantified using the Functional Magnetic Resonance Imaging of the Brain (FMRIB) Software Library (FSL) FIRST procedure and scaled by intracranial volume. The effects on regional volume of age, sex, puberty, and their interactions were examined using linear regression. Postpubertal sex differences were examined using a vertex analysis. Prepubertal males and females had similar hippocampal volumes, whereas postpubertal females had significantly larger bilateral hippocampi, resulting in a significant puberty-by-sex interaction even when controlling for age and age-by-sex. This effect was regionally specific and was not apparent in the amygdala. Vertex analysis revealed that postpubertal differences were most prominent in the lateral aspect of the hippocampus bilaterally, corresponding to the CA1 subfield. These results establish that there are regionally specific sex differences in the effect of puberty on the hippocampus. These findings are relevant for the understanding of psychiatric disorders that have both hippocampal dysfunction and prominent gender disparities during adolescence.