Cross-sectional geometry of ancient Jomon femora were analyzed along the whole shaft by means of computed tomography. Comparisons were made with modern Japanese (from the same geographical area as the Jomon people) and recent Germans (of larger body size and from a geographical area distant from Japan). Jomon male femora were significantly larger than those of modern Japanese males along the whole shaft length in cross-sectional area (A), polar second moment of area (Ip), second moment of area around the mediolateral direction (Ix), maximum second moment of area (Imax), and cross-sectional index of radii of gyration (kx/ky). These parameters were about the same magnitude in the Jomon males, as in the German males whose size was large, except for the second moment of area around the anteroposterior direction (Iy), which was smaller in the Jomon bones. Female Jomon femora showed the same tendency but only at the middle part of the shaft. There were allometric correlations between bone length and the geometrical properties. In order to eliminate the influence of size, relative dimensionless properties were calculated by dividing each parameter by an analogue of length, namely A was divided by maximum length squared, and Ip, Ix, Iy, Imax, and Imin were divided by the fourth power of the maximum length. The German femora of both sexes were smaller than those of the Jomon in relative area, relative Ix, and relative Ip. Male Jomon femora contained a large volume of bone substance and were robust against bending moments especially in the anteroposterior direction along the whole shaft when comparison was made with other modern or recent groups. These characteristics are less definitive with female bones. They were caused as a functional adaptation for sedentary gatherer-hunters.