Over the past four decades, our understanding of swallowing neural control has expanded dramatically. However, until recently, advances in rehabilitation approaches for dysphagia have not kept pace, with a persistent focussing on strengthening peripheral muscle. This approach is no doubt very appropriate for some if not many of our patients. But what if the dysphagia is not due to muscles weakness? The purpose of this clinical manuscript is to reflect on where we have been, where we are now and perhaps where we need to go in terms of our understanding of swallowing motor control and rehabilitation of motor control impairments. This compilation is presented to clinicians in the hope that suggesting approaches “outside the box” will inspire clinicians to focus their attention “inside the box” to ultimately improve rehabilitation and long-term outcomes for patients with dysphagia.