Lots of researchers take great interests in brain science. In this area, measurement devices of the brain have been developed by number of groups, and played an important role. Recently, for neuroengineering applications such as optogenetics, optical stimulation devices which consisted of optical fibers have been reported, and used to deliver light to neurons expressing light sensitive channel proteins. However, accurate stimulation of neurons could not be achieved by using these devices because of optical fibers with a diameter of over 100 m. Here, we have proposed a novel Si neural probe with micromachined optical waveguide for multiple and precise optical stimulations of neurons. SiN film was employed as the optical waveguide core due to its optical transmission characteristics. Both the light propagation in the optical waveguide and controllability of output patterns of the light were clearly confirmed by optical experiments using a blue laser. In vitro experiments of optical stimulation of neurons using the fabricated Si neural probe were performed. A CA1 area of a thin hippocampal slice obtained from the brain of a transgenic rat expressing Channelrhodopsin-2 (ChR2) was employed. We stimulated neurons optically using the Si neural probe and successfully observed increases of firing rates in neurons accordingly with the light exposure.