The aims of this study are to examine the human skeletal remains from the Yuigahama-chusei-shudan-bochi (seika-ichiba) site, or YCSB-SI, to provide data regarding the metrics of the crania and limb bones, to compare these metrics with those of ancient Japanese skeletons, and to discuss the population variability of the medieval Japanese. The results provided several findings regarding the cranial and limb-bone traits of the YCSB-SI sample: (1) the YCSB-SI remains shared dolichocephaly with the remains from the other medieval series, but the YCSB-SI remains had the highest faces of all the medieval series; (2) there is a distinction between the YCSB-SI remains and the Jomon remains in that the former had a larger length–breadth index of the crania, higher Virchow’s facial and upper facial indices, smaller maximum length of the ulnae and tibiae, and a smaller mid-shaft index of the femora than the latter; and (3) the estimated stature from Fujii’s equations using the maximum length of the femur for YCSB-SI males and females was 158.7 and 146.3 cm, respectively, which is nearly equal to that of other medieval series but several centimeters shorter than that of the Kofun series.