Photons with a great many tunable physical properties have been profoundly engaged in research of brain science in all aspects for more than a hundred years. Taking advantage of highly developed incoherent light sources, coherent lasers and short-pulse lasers, innovative optical tools including both instrumentations and strategies have significantly boosted comprehensive research on neural science within a very short period. Right before China launches its Brain Project (Chinese version of BRAIN — Brain Research through Advancing Innovative Neurotechnologies) by the end of this year (2017), we are delighted to introduce to our readers a special issue on applications of bio-photonics in neuroscience and brain diseases.