Detailed knowledge of the loading conditions within the human body is essential for the development and optimization of treatments for disorders and injuries of the musculoskeletal system. While loads in the major joints of the lower limb have been the subject of extensive study, relatively little is known about the forces applied to the individual bones of the foot. The objective of this study was to use a detailed musculoskeletal model to compute the loads applied to the metatarsal bones during gait across several healthy subjects. Motion-captured gait trials and computed tomography (CT) foot scans from four healthy subjects were used as the inputs to inverse dynamic simulations that allowed the computation of loads at the metatarsal joints. Low loads in the metatarsophalangeal (MTP) joint were predicted before terminal stance, however, increased to an average peak of 1.9 times body weight (BW) before toe-off in the first metatarsal. At the first tarsometatarsal (TMT) joint, loads of up to 1.0 times BW were seen during the early part of stance, reflecting tension in the ligaments and muscles. These loads subsequently increased to an average peak of 3.0 times BW. Loads in the first ray were higher compared to rays 2–5. The joints were primarily loaded in the longitudinal direction of the bone.