Objectives The Jomon people were hunter‐gatherers who inhabited the Japanese archipelago between 10,000 BC and 300 BC. Here, we focus on the mid‐shaft cross‐sectional shape of the ulna in the Jomon population and compare it with modern Japanese people. Materials and methods Jomon specimens, including 32 males and 22 females, were excavated from shell mound sites in the Pacific and Seto inland coastal area of Honshu island in the Japanese archipelago dated to the Late‐to‐Final Jomon phase (between 2,000 BC and 300 BC). Mid‐shaft ulna cross‐sectional shapes were compared with modern Japanese specimens (25 males, 21 females) using standard linear measurements and elliptic Fourier analysis (EFA). Differences from both sides of this element were compared using predicted handedness. Results Linear measurements and EFA results show that ulna shape of both sexes within the Jomon population are relatively larger in the antero‐posterior direction and have more developed posterior borders than modern Japanese males and females. No significant differences were observed between Jomon sexes based on the predicted dominant side, but differences were evident in the predicted nondominant side. At the same time, bilateral differences were recognized in Jomon females, because of a lower level of posterior border development in the predicted nondominant side compared to the dominant side. Discussion Shape differences between Jomon people and modern Japanese can be explained by variation in the habitual loading of the ulna. Sexual dimorphism in ulna shape within the Jomon population suggests division of labor differences.