Objective Although neuroimaging studies have shown volumetric reductions, such as the anterior cingulate, prefrontal cortices, and hippocampus in patients with major depressive disorder (MDD), few studies have investigated the volume of or shape alterations in the subcortical regions and the brainstem. We hypothesized that medication-naïve female adult patients with MDD might present with shape and volume alterations in the subcortical regions, including the brainstem, compared to healthy controls (HCs). Methods A total of 20 medication-naïve female patients with MDD and 21 age-matched female HCs, underwent 3D T1-weighted structural magnetic resonance scanning. We analyzed the volumes of each subcortical region and each brainstem region, including the midbrain, pons, and medulla oblongata. We also performed surface-based vertex analyses on the subcortical areas and brainstem. Results Female patients with MDD showed non-significant volumetric differences in the subcortical regions, whole brainstem, and each brainstem region compared to the HCs. However, in the surface-based vertex analyses, significant shape contractions were observed in both cerebellar peduncles located on the lateral wall of the posterior brainstem [threshold-free cluster enhancement, corrected for family-wise error (FWE) at p<0.05] in patients with MDD. Conclusion We revealed shape alterations in the posterior brainstem in female patients with MDD.