Skipping has been proposed as a viable cross-training exercise to running due to its lower knee contact forces and higher whole-body energy expenditure. However, how individual muscle forces, energy expenditure, and joint loading are affected by differences in running and skipping mechanics remains unclear. The purpose of this study was to compare individual muscle forces, energy expenditure, and lower extremity joint contact forces between running and skipping using musculoskeletal modeling and simulations of young adults (n = 5) performing running and skipping at 2.5m·s-1 on an instrumented treadmill. In agreement with previous work, running had greater knee and patella contact forces than skipping which was accompanied by greater knee extensor energetic demand. Conversely, skipping had greater ankle contact forces and required greater energetic demand from the uniarticular ankle plantarflexors. There were no differences in hip contact forces between gaits. These findings further support skipping as a viable alternative to running if the primary goal is to reduce joint loading at the commonly injured patellofemoral joint. However, for those with ankle injuries, skipping may not be a viable alternative due to the increased ankle loads. These findings may help clinicians prescribe activities most appropriate for a patient's individual training or rehabilitation goals.