High frequency stimulations (HFS) of electrical pulses with different durations have different effects on the nervous system in brain. A short HFS train with a duration of several seconds can be used to establish epilepsy models in animals via a “kindling” effect. It can also produce changes of synaptic plasticity that may persist. However, a long HFS train with a duration several minutes or longer can be safely applied in deep brain stimulation to treat various brain diseases in clinic. Therefore, we speculate that a sustained HFS could change the neuronal responses induced by a short HFS. To verify this hypothesis, 100 Hz HFS with durations of 5 s and 2 min were applied to the Schaffer collateral of afferent fibers in the hippocampus CA1 region of rats. The response potentials of downstream populations of neurons, i.e., population spikes (PS), evoked by a single test pulse were monitored after the termination of HFS trains. The evoked-PS potentials following the two types of stimulation were compared. The results showed that after-discharge events with epileptiform activity appeared immediately following 5 s short HFS trains. In addition, the changes of amplitude and latency of the evoked-PS suggest an increase of excitability persisting for tens of minutes after the termination of 5 s short HFS. In contrast, silent periods of a few tens of seconds without any neuronal firing appeared immediately following 2 min long HFS trains. Furthermore, the amplitude of evoked-PS by test pulses recovered to the baseline level in a few minutes after the termination of long HFS. Because long HFS trains include short HFS trains, these results indicate that the late stimulation of long trains can change the effects on the downstream neural networks produced by their early phases and eliminate the long-term excitatory effects induced by short trains. These findings are of significance for further revealing HFS mechanisms and for advancing the clinical applications of deep brain stimulation.