Purpose: Deep Brain Stimulation (DBS) of the hippocampus is an experimental treatment for medically refractory epilepsy. The optimal stimulation parameters are yet to be explored. High frequency hippocampal DBS (HFS) proved to be effective in both epileptic patients and animals. Furthermore, low frequency stimulation (LFS) is assumed to have anti-epileptic properties but this is highly debated. This animal study compares the effects of both stimulation modalities in kindled rats. Methods: Rats (n = 20) were fully kindled in the hippocampus according to the Alternate Day Rapid Kindling model. After a baseline kindling period, rats were divided into a 130Hz HFS group (n = 11) and a 5Hz LFS group (n = 9) receiving 10 days of continuous DBS. During and after termination of DBS, all rats received seizure-evoking kindling stimuli. Characteristics of the evoked afterdischarges (AD) were compared between both treatment groups. Results: During HFS, the AD threshold and the AD latency were significantly more increased (p < 0.05 and p < 0.005 respectively) compared with baseline than during LFS (p = 0.48 and p = 0.05 respectively) compared with baseline. Only for HFS-treated rats, the AD duration was shorter (p < 0.05) during treatment. After termination of DBS, all effects fade out slowly, only the AD threshold becomes more elevated in the LFS group. Conclusion: Both high and low frequency stimulation of the hippocampus in epileptic rats result in a reduced excitability. Comparing HFS with LFS indicates that 130Hz stimulation is more effective in comparison with 5Hz stimulation, which is reflected in a higher AD threshold and AD latency, and a shorter AD duration during treatment.