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Treatments for epilepsy include pharmacotherapy or surgery. Recently, focused ultrasound stimulation has been investigated as a promising non-invasive neuromodulation tool for neurological disorders, including epilepsy. To investigate the neuronal dynamics in epilepsy, we acutely stimulated 29 Sprague–Dawley rats to low-intensity focused ultrasound stimulation (LIFUS) three times for 3 minutes. Pentylenetetrazol (PTZ) was injected into the abdominal cavity of the anesthetized rats to induce epilepsy. During the anesthesia, the electroencephalography (EEG) signal was measured and analyzed for 1 h in groups of animals untreated (sham) and treated with LIFUS. The EEG signal was quantitatively processed to show the different characteristics of the frequency change over time and of the band power between sham and treated groups. Histological analyses (Nissl, Iba1, c-Fos, and GAD65) measured the degree of staining of expression factors to confirm the effect of the stimulation on seizure suppression. These results suggest that repetitive LIFUS can effectively reduce epileptic seizure activity by attenuating theta and beta-band oscillation in a PTZ-induced rat model. LIFUS can potentially facilitate hippocampal and cortical cellular recovery by augmenting GABAergic inhibitory neurons via its anti-seizure effect.