Estimating kinematics from optical motion capture with skin-mounted markers, referred to as an inverse kinematic (IK) calculation, is the most common experimental technique in human motion analysis. Kinematics are often used to diagnose movement disorders and plan treatment strategies. In many such applications, small differences in joint angles can be clinically significant. Kinematics are also used to estimate joint powers, muscle forces, and other quantities of interest that cannot typically be measured directly. Thus, the accuracy and reproducibility of IK calculations are critical. In this work, we isolate and quantify the uncertainty in joint angles, moments, and powers due to two sources of error during IK analyses: errors in the placement of markers on the model (marker registration) and errors in the dimensions of the model’s body segments (model scaling). We demonstrate that IK solutions are best presented as a distribution of equally probable trajectories when these sources of modeling uncertainty are considered. Notably, a substantial amount of uncertainty exists in the computed kinematics and kinetics even if low marker tracking errors are achieved. For example, considering only 2 cm of marker registration uncertainty, peak ankle plantarflexion angle varied by 15.9°, peak ankle plantarflexion moment varied by 26.6 N⋅m, and peak ankle power at push off varied by 75.9 W during healthy gait. This uncertainty can directly impact the classification of patient movements and the evaluation of training or device effectiveness, such as calculations of push-off power. We provide scripts in OpenSim so that others can reproduce our results and quantify the effect of modeling uncertainty in their own studies.