A thermomechanical model for predicting the steady state temperature of a rotating, misaligned composite shaft is developed, in which it is assumed that all strain energy loss caused by internal damping is converted into heat. The composite shaft is modeled as a laminated, anisotropic tube subjected to cyclic pure bending loads. The temperature profile through the radius of the shaft is modeled using the finite difference method. Inputs to the model are the ply configuration of the shaft, shaft misalignment strain, shaft rotation speed, and lamina elastic and damping properties. A lab-scale shaft spin testing stand was built to validate the self-heating model. Good agreement is shown between the model predictions and experiment results. It is found the temperature increase caused by self-heating during the misaligned rotation increases with increasing shaft speed and, more significantly, misalignment strain. It is also found that the self-heating of a FMC shaft can be less significant than that of an equivalent rigid matrix composite shaft despite the fact that the former has a much higher internal damping than the latter. This model can be valuable in the selection of constituent materials for FMCs and also in the design of FMC shafts.