Peripheral joint injuries (PJI) can result in biomechanical disturbances as well as chronic neuromuscular alterations due in part to loss of mechanoreceptor-mediated afferent feedback. An emerging perspective is that PJI should be viewed as a neurophysiological dysfunction, not simply a local injury. Neurophysiological and neuroimaging studies have provided some evidence for central nervous system (CNS) reorganization at both cortical and spinal levels following peripheral joint injuries. The novel hypothesis proposed is that CNS reorganization is the underlying mechanism for persisting neuromuscular deficits following injury, in particular, muscle weakness. There is a lack of direct evidence to support this hypothesis, but future studies utilizing force-matching tasks with superimposed transcranial magnetic stimulation could be a step forward in clarifying this notion.