He is known for creating and developing the technologies of hydrogel-tissue chemistry (e.g., CLARITY, STARmap) and optogenetics, and for applying integrated optical and genetic strategies to study normal neural circuit function, as well as dysfunction in neurological and psychiatric disease.

In 2019, Deisseroth was elected as a member of the US National Academy of Engineering for molecular and optical tools for his discovery and control of neuronal signals behind animal behavior in health and disease.

[citation needed] He serves as an attending physician at Stanford Hospital and Clinics and has been affiliated with the Howard Hughes Medical Institute (HHMI) since 2009.

In 2016, Deisseroth received the Massry Prize along with Peter Hegemann and Miesenböck for "optogenetics, a technology that utilizes light to control cells in living tissues".

[10] Finally in 2020, Deisseroth received the Heineken Prize from the Royal Netherlands Academy of Arts and Sciences, "for developing optogenetics — a method to influence the activity of nerve cells with light".

[15] Two major prizes paid particular attention to Deisseroth's work on elucidation of the structure and function of light-gated ion channels—the 2016 Harvey Prize to Deisseroth and Hegemann for the "discovery of opsin molecules, involved in sensing light in microorganisms, and for the pioneering work in utilizing these opsins to develop optogenetics",[7] and the 2018 Gairdner Award, which noted "his group discovered the fundamental principles of the unique channelrhodopsin proteins in molecular detail by a wide range of genomic, biophysical, electrophysiological and structural techniques with many mutants in close collaboration with Peter Hegemann").

Deisseroth has published the notebook pages from early July 2004 of his initial experiment showing light activation of neurons expressing a channelrhodopsin.