Recent advances in optogenetics, which optically regulate biological processes by using genetically engineered proteins, have shown its importance and potential. Optogenetics has shown many applications in various research fields ranging from neuroscience and cardiology to genetics. While optogenetics has advantages in in vivo functional studies, multiple light scattering caused by biological tissues such as brain or skull layers significantly prevents non-invasive in vivo applications. To overcome aforementioned issue resulted from multiple light scattering, invasive approaches including implementation of endoscopes or optical fibers and cranial windows have been used. While invasive methods provide deep light penetration, it inevitably causes deleterious effects on tissues. Recently, genetically modified proteins which response to near-infrared (NIR) light have been developed, but penetration depths of NIR light is still limited to a few millimeter. Toward the development of non-invasive in vivo optogenetic applications, we exploited a wavefront shaping method. We demonstrated that an illumination with shaped waves make a focus through a scattering skull, and it enables spatiotemporal control of intracellular Ca2+ concentrations by activating photoactivatable proteins.