Voltage-gated sodium channels (Na) are closely associated with epilepsy, cardiac and skeletal muscle diseases, and neuropathic pain. Several toxic compounds have been isolated from the marine sponge ; however, toxic substances that modulate Na are yet to be identified. This study aimed to identify Na inhibitors from two snake venoms and using mouse neuroblastoma Neuro-2A cells (N2A), which primarily express the specific Na subtype Na1.7, using whole-cell patch-clamp recordings. We successfully isolated arachidonic acid (AA, ) from the hexane extract of , and then the fatty acid-mediated modulation of Na in N2A was investigated in detail for the first time. Octanoic acid (), palmitic acid (), and oleic acid () showed no inhibitory activity at 100 μM, whereas AA (), dihomo-γ-linolenic acid (DGLA, ), and eicosapentaenoic acid (EPA, ) showed IC values of 6.1 ± 2.0, 58 ± 19, and 25 ± 4.0 μM, respectively ( = 4, mean ± SEM). Structure and activity relationships were investigated for the first time using two ω-3 polyunsaturated fatty acids (PUFAs), EPA () and eicosatetraenoic acid (ETA, ), and two ω-6 PUFAs, AA () and DGLA (), to determine their effects on a resting state, activated state, and inactivated state. Steady-state analysis showed that the half inactivation potential was largely hyperpolarized by 10 μM AA (), while 50 μM DGLA (), 50 μM EPA (), and 10 μM ETA () led to a slight change. The percentages of the resting state block were 24 ± 1, 22 ± 1, 34 ± 4, and 38 ± 9% in the presence of AA (), DGLA (), EPA (), and ETA (), respectively, with EPA () and ETA () exhibiting a greater inhibition than both AA () and DGLA (), and their inhibitions did not increase in the following depolarization pulses. None of the compounds exhibited the use-dependent block. The half recovery times from the inactivated state for the control, AA (), DGLA (), EPA (), and ETA () were 7.67 ± 0.33, 34.3 ± 1.10, 15.5 ± 1.10, 10.7 ± 0.31, and 3.59 ± 0.18 ms, respectively, with AA () exhibiting a distinctively large effect. Overall, distributed binding to the resting and the inactivated states of Na would be significant for the inhibition of Na, which presumably depends on the active structure of each PUFA.