While many children suffer from stress due to school-related factors, some alternative schooling systems, such as the Montessori pedagogy, emphasize stress-free learning environments (e.g., no grades, no tests, peer-peer learning). This study compared brain markers of stress, i.e., hippocampus, amygdala, and medial prefrontal cortex (mPFC) volumes, as a function of school experience. A cross-sectional comparative morphometric study was run between 45 traditionally schooled children and 44 Montessori-schooled children (3-12 years). While both groups were comparable in terms of cognitive abilities, socio-economic environment, and anxiety levels, volumetric values within their hippocampus and their mPFC differed. While there was hippocampal growth across development for all participants, there was a higher gain for Montessori-schooled children. Furthermore, female traditionally schooled children showed a loss in hippocampal and mPFC volume across age, while female Montessori-schooled children showed a gain. It seems that traditional pedagogical approaches induce mild but chronic stress, affecting underlying brain structures.