The aim of this cross-sectional study was to investigate whether physical activity and bone status may affect arterial thickening and stiffening in healthy Japanese women. Healthy women (n = 149; mean age, 54 years) were recruited from those who participated in a local health check program at the Osaka City University Hospital. Physical activity was assessed by physical functioning score of SF-36, and bone status by bone mineral density (BMD) in lumbar spine and calcaneus osteo-sono index (OSI). Arterial wall thickening assessed by intima-media thickness (IMT) in common carotid artery (CA) and femoral artery (FA), and arterial wall stiffening by peak wave velocity (PWV) in heart-carotid (hc) and heart-femoral (hf) as central segment and in heart-brachial (hb) and femoral-ankle (fa) as peripheral segment, respectively. By Spearman Rank correlation, lumbar spine BMD was correlated negatively with CA IMT (rho = -0.225, p < 0.05) and FA IMT (rho = -0.215, p < 0.05), and calcaneus OSI with FA IMT (rho = -0.330, p < 0.0001) but not CA IMT (rho = -0051, p = 0.5335). Both lumbar spine BMD and calcaneus OSI correlated negatively with PWV in all segments (all p < 0.05). Physical functioning score correlated weakly but significantly in a negative manner with all PWV segments (all p < 0.05) but not IMT. Multiple regression analyses revealed a significant association of calcaneus OSI (beta = -0.240, p = 0.0039) but not lumbar spine BMD (beta = -0.067, p = 0.4541) with FA IMT, although neither lumbar spine BMD nor calcaneus OSI was associated with CA IMT. Furthermore, physical functioning score was independently associated with hb and fa PWV but not hc and hf PWV, suggesting the preferential association with peripheral segment including lower extremities. Neither lumbar spine BMD nor calcaneus OSI was associated with any segment of PWV. In conclusion, it was suggested that calcaneus OSI might be associated with arterial wall thickening preferentially in femoral artery, and that physical activity may be associated with arterial wall stiffening in peripheral segment including lower extremity but not in central segment in healthy Japanese women.