Key points• Kv3 channels play a critical role in neuronal fast spiking and their regulation can profoundly influence the functions of various neural circuits.• Zinc reversibly inhibits fast spiking in cultured neurons by inhibiting Kv3 channels. Surprisingly, we found that the zinc inhibition is not through its known site in the N-terminal T1 domain of Kv3.1.• We have identified a new zinc-binding site in the Kv3.1 C-terminus, involved in regulating channel activity and targeting, but not the zinc inhibition.• We have also identified the junction between the first transmembrane segment and the first extracellular loop as the major zinc-sensing site in regulating Kv3 activity. This result allows us to reconstitute zinc-resistant fast spiking.• Kv3 channel assembly, localization and activity are regulated by zinc through intracellular and extracellular binding sites.Abstract Zinc, a divalent heavy metal ion and an essential mineral for life, regulates synaptic transmission and neuronal excitability via ion channels. However, its binding sites and regulatory mechanisms are poorly understood. Here, we report that Kv3 channel assembly, localization and activity are regulated by zinc through different binding sites. Local perfusion of zinc reversibly reduced spiking frequency of cultured neurons most likely by suppressing Kv3 channels. Indeed, zinc inhibited Kv3.1 channel activity and slowed activation kinetics, independent of its site in the N-terminal T1 domain. Biochemical assays surprisingly identified a novel zinc-binding site in the Kv3.1 C-terminus, critical for channel activity and axonal targeting, but not for the zinc inhibition. Finally, mutagenesis revealed an important role of the junction between the first transmembrane (TM) segment and the first extracellular loop in sensing zinc. Its mutant enabled fast spiking with relative resistance to the zinc inhibition. Therefore, our studies provide novel mechanistic insights into the multifaceted regulation of Kv3 channel activity and localization by divalent heavy metal ions.