In many aerospace applications, it is impossible to measure the forces, both aerodynamic and structure-borne, applied to a structure in its service environment. Furthermore, collecting service environment data requires a modified flight structure which accommodates telemetry equipment. Due to the different mechanical impedances of the shaker table and payload, the test structure experiences different loads in the test environment which can lead to over- and undertesting of the structure. Consequently, force-controlled testing may be a more desirable testing procedure as it more accurately reflects the service environment and eliminates the adverse effects caused by the differences in mechanical impedance. As part of this procedure, a numerical model is required to derive the test forces to replace the acceleration control. Determining these test forces from the model will introduce uncertainty into the flight structure’s response profile. This paper aims to quantify the uncertainty in the determination of the test forces used in the force-controlled test and the uncertainty in the test structure’s response.