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Pathologic movement patterns are characterized by abnormal kinematics that alter how muscles support the body during walking. Individual muscles are often the target of interventions with physical therapy and surgery alike, yet the tools to assess individual muscles clinically remain limited. The aim of this study is to assess OpenSim as a clinical tool for individualized rehabilitative evaluation of children using orthotics. This anatomic and kinematic modeling study was focused on pre- and post-treatment assessment of gait characteristics in fourteen children using orthotic devices. A range of four to twelve acceptable gait capture trials was collected for each child before therapy began and again after four weeks of treatment. The effects of therapy were significant in four of the lower extremity muscle analyses, three of the temporal parameters, and eighteen of the spatial parameters. All muscle lengths showed less deviation from normal values after physical therapy across all subjects. Results of this study support the further evaluation of OpenSim as a tool to improve quantitative assessment of musculoskeletal dynamics during the course of rehabilitative therapy in children using orthotics.