Motor movement is controlled by the brain through transmitting electrochemical signals to the muscle fibers that cause the contraction of the muscles. A motoneuron carrying the impulse creates a synapse with the muscle fiber which is known as Neuromuscular Junction (NMJ). The muscle infolds taking part in the synapse contains large amount of sodium channels. The current that passes through the narrow synaptic cleft affects the adjacent membranes electrical properties in turn modifies the synaptic transmission process. Considering this phenomenon we have studied the effect of sodium channels at the NMJ to find out its effect in the generation of extracellular potentials at the synaptic cleft of the junction. Through simulation results we confirm that the conductivity of the sodium channels present at the postsynaptic muscle membrane and the junction height affect the generation of the extracellular potentials at the junction which modifies the synaptic properties of the NMJ.