Optogenetics is a novel strategic field that combines light (opto-) and genetics (genetic) into applications able to control the activity of excitable cells and neuronal circuits. Using genetic manipulation, optogenetics may induce the coding of photosensitive ion channels on specific neurons: this non-invasive technology combines several approaches that allow users to achieve improved optical control and higher resolution. This technology can be applied to optical systems already present in the clinical-diagnostic field, and it has also excellent effects on biological investigations and on therapeutic strategies. Recently, several biomedical applications of optogenetics have been investigated, such as applications in ophthalmology, in bone repairing, in heart failure recovery, in post-stroke recovery, in tissue engineering, and regenerative medicine (TERM). Nevertheless, the most promising and developed applications of optogenetics are related to dynamic signal coding in cell physiology and neurological diseases. In this review, we will describe the state of the art and future insights on the impact of optogenetics on regenerative medicine.