Adult Jomon femora are known to be more robust with mid-diaphyseal cross sections that are more elongated anteroposteriorly than in the modern Japanese. In the present study, we compared femoral midshaft cross-sectional geometric properties between prehistoric Jomon hunter-gatherers and modern Japanese from the seventh fetal month to 17 years of age. The cross-sectional properties reflecting mechanical strength and shape (e.g. cortical bone area, medullary cavity area, area moments of inertia, representative indices) were measured using micro-computed tomography on 58 Jomon and 73 modern Japanese femora. Results showed that the Jomon midshaft cross sections are significantly larger, more robust, and stronger under mechanical loading than those of the modern Japanese throughout the examined fetal to subadult periods. The consistently greater robusticity of the Jomon femur was caused by (1) greater bone diameter and mass established at least by late fetal life, (2) lower endosteal bone resorption rates from toddler through subadult ages, and (3) greater subperiosteal bone expansion after around puberty. In both Jomon and modern Japanese, the femoral midshaft cross-sectional shape changes through growth, on average, from near-circular to slightly anteroposteriorly elongated. This was seen to be exaggerated in the Jomon midshaft by bone distributional changes that involve enhanced posterior projection of the shaft corresponding to the well-known femoral shaft pilaster. The results also demonstrated that the fetal to infant Jomon femoral midshaft cross sections tend to be broader mediolaterally than those of the modern Japanese, possibly contributing to the adult subtrochanteric platymeric (mediolaterally broad) cross-sectional shape of the Jomon proximal femoral shaft. Our findings suggest that complex interactions of population-specific genetic background, differential response to activity level and/or mechanical load, and elevated levels of activity/load and muscle hypertrophy appear to have caused the Jomon condition of a comparatively robust femoral diaphysis.