Fast inactivation of voltage-gated sodium (Nav) channels is essential for electrical signaling but its mechanism remains poorly understood. Here, we determined the structures of a eukaryotic Nav channel alone and in complex with a lethal α-scorpion toxin, AaH2, by electron microscopy, both at 3.5-A resolution. AaH2 wedges into voltage-sensor domain IV (VSD4) to impede fast activation by trapping a deactivated state in which gating charge interactions bridge to the acidic intracellular C-terminal domain. In the absence of AaH2, the S4 helix of VSD4 undergoes a ~13-Å translation to unlatch the intracellular fast inactivation gating machinery. Highlighting the polypharmacology of α-scorpion toxins, AaH2 also targets an unanticipated receptor site on VSD1 and a pore-glycan adjacent to VSD4. Overall, this work provides key insights into fast inactivation, electromechanical coupling, and pathogenic mutations in Nav channels.