Neuromusculoskeletal injuries including osteoarthritis, stroke, spinal cord injury, and traumatic brain injury affect roughly 19% of the U.S. adult population. Standardized interventions have produced suboptimal functional outcomes due to the unique treatment needs of each patient. Strides have been made to utilize computational models to develop personalized treatments, but researchers and clinicians have yet to cross the “valley of death” between fundamental research and clinical usefulness. This article introduces the Neuromusculoskeletal Modeling (NMSM) Pipeline, two MATLAB-based toolsets that add Model Personalization and Treatment Optimization functionality to OpenSim. The two toolsets facilitate computational design of individualized treatments for neuromusculoskeletal impairments through the use of personalized neuromusculoskeletal models and predictive simulation. The Model Personalization toolset contains four tools for personalizing 1) joint structure models, 2) muscle–tendon models, 3) neural control models, and 4) foot–ground contact models. The Treatment Optimization toolset contains three tools for predicting and optimizing a patient’s functional outcome for different treatment options using a patient’s personalized neuromusculoskeletal model and direct collocation optimal control methods. Support for user-defined cost, constraint, and model modification functions facilitate simulation of a vast number of possible treatments. An NMSM Pipeline use case is presented for an individual post-stroke with impaired walking function, where the goal was to predict how the subject’s neural control could be changed to improve walking speed without increasing metabolic cost. First the Model Personalization toolset was used to develop a personalized neuromusculoskeletal model of the subject starting from a generic OpenSim full-body model and experimental walking data (video motion capture, ground reaction, and electromyography) collected from the subject at his self-selected speed. Next the Treatment Optimization toolset was used with the personalized model to predict how the subject could recruit existing muscle synergies more effectively to reduce muscle activation disparities between the paretic and non-paretic legs. The software predicted that the subject could increase his walking speed by 60% without increasing his metabolic cost per unit time by modifying existing muscle synergy recruitment. This hypothetical treatment demonstrates how NMSM Pipeline tools could allow researchers working collaboratively with clinicians to develop personalized neuromusculoskeletal models of individual patients and to perform predictive simulations for designing personalized treatments that maximize a patient’s post-treatment functional outcome.