Considerable effort in recent years has been devoted to investigating neurophysiological changes in the brain after stroke and in developing novel strategies to enhance recovery particularly in the limbs and trunk. In contrast, although dysphagia is a severe complication and can be life threatening in a considerable number of stroke patients, it has not yet received the attention devoted to limb control. In this review, we discuss how introduction of (a) transcranial magnetic stimulation (TMS) to test noninvasively the integrity of the cortico-bulbar swallowing system and (b) the plasticity provoking protocols of rTMS and transcranial direct current stimulation have recently stimulated research into dysphagia after stroke and led to new potential avenues for treatment. We discuss the neural control of swallowing and discuss the contributions of TMS to understand how different brain areas are involved in dysphagia. We also consider recent studies using noninvasive brain stimulation to interact with synaptic plasticity in cortex and enhance recovery of dysphagia following stroke. Although further studies are needed, these investigations provide an important starting point to understand the stimulation parameters and patient characteristics that may influence the optimal response to therapeutic noninvasive brain stimulation. These techniques need to be refined further through a multicenter study so that they can become an essential tool that can be used in academic centers of excellence as well as in a general hospital setting.