The glossopharyngeal nerve (N.IX) transfers motor and sensory information related to visceral and somatic functions, such as salivary secretion, gustation and the control of blood pressure. N.IX-related neural circuits are indispensable for these essential functions. Compared with the strenuous analysis of morphogenesis, we are only just starting to elucidate the functiogenesis of these neural circuits during ontogenesis. In the present study, we applied voltage-sensitive dye recording to the embryonic mouse brainstem, and examined the functional development of the N.IX-related neural circuits. First, we optically identified the motor nucleus (the inferior salivatory nucleus (ISN)) and the first-order sensory nucleus (the nucleus of the tractus solitarius (NTS)). We also succeeded in recording optical responses in the second/higher-order sensory nuclei via the NTS, including the parabrachial nucleus. Second, we pursued neuronal excitability and the onset of synaptic function in the N.IX-related nuclei. The neurons in the ISN were excitable at least at E11, and functional synaptic transmission in the NTS was first expressed at E12. In the second/higher-order sensory nuclei, synaptic function emerged at around E12-13. Third, by mapping optical responses to N.IX and vagus nerve (N.X) stimulation, we showed that the distribution patterns of neural activity in the NTS were different between the N.IX and the N.X from the early stage of ontogenesis. We discuss N.IX-related neural circuit formation in the brainstem, in comparison with our previous results obtained from chick and rat embryos.