3'-5'-Cyclic AMP (cAMP) is an important second messenger which regulates neurite outgrowth. We demonstrate here that type VI adenylyl cyclase (AC6), an enzyme which catalyzes cAMP synthesis, regulates neurite outgrowth by direct interaction with a binding protein (Snapin) of Snap25 at the N terminus of AC6 (AC6-N). We first showed that AC6 expression increased during postnatal brain development. In primary hippocampal neurons and Neuro2A cells, elevated AC6 expression suppressed neurite outgrowth, whereas the downregulation or genetic removal of AC6 promoted neurite extension. An AC6 variant (AC6-N5) that contains the N terminus of AC5 had no effect, indicating the importance of AC6-N. The downregulation of endogenous Snapin or the overexpression of a Snapin mutant (Snap(Δ33-51)) that does not bind to AC6, or another Snapin mutant (Snapin(S50A)) that does not interact with Snap25, reversed the inhibitory effect of AC6. Pulldown assays and immunoprecipitation-AC assays revealed that the complex formation of AC6, Snapin, and Snap25 is dependent on AC6-N and the phosphorylation of Snapin. The overexpression of Snap25 completely reversed the action of AC6. Collectively, in addition to cAMP production, AC6 plays a complex role in modulating neurite outgrowth by redistributing localization of the SNARE apparatus via its interaction with Snapin.