Mesial temporal lobe epilepsy (MTLE) is one of the most common forms of human epilepsy, and it is often resistant to conventional antiepileptic drug (AED) therapy. Here we tested whether a single intrahippocampal administration of the synaptic blocker botulinum neurotoxin E (BoNT/E) is effective in reducing spontaneous recurrent seizures (SRS) in a mouse model of MTLE. Unilateral intrahippocampal injection of kainic acid (KA) in mice was used as a model of MTLE. Electroencephalography (EEG) recordings of SRS were performed during the chronic phase of epilepsy, before and after administration of either BoNT/E or vehicle. Frequency of SRS was significantly decreased for at least 5 days following BoNT/E, but not vehicle, infusion. Our findings demonstrate that BoNT/E can effectively reduce seizure incidence in a mouse model of MTLE.