Specific subcellular targeting and spatial arrangement of signaling molecules are important for efficient signal transduction. The neuro-specific type-I adenylyl cyclase (AC1) is stimulated by Ca2+, and plays an essential role in neurodevelopment and neuroplasticity. We generated hemagglutinin (HA)-tagged AC1 to study its subcellular localization in cultured neurons. The HA-tagged AC1 has similar enzymatic activity and regulatory properties to that of non-tagged protein. HA-AC1 targeted to both apical and basolateral domains in the epithelial Madin-Darby canine kidney (MDCK) cells, and it was found in both axons and dendrites in cultured hippocampal neurons as well as in cerebellar granule neurons. Interestingly, AC1 showed a distinct punctate form of immunostaining in MDCK cells and transfected neurons, suggesting it targets to specific subcellular domains. By immunostaining with different synaptic markers, we found that AC1 puncta were located at the excitatory synapses in cerebellar granule neurons. Our data provide a possible cellular mechanism for the physiological role of AC1 in neuroplasticity.