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Sequences of electrical pulses have been applied in the brain to treat certain disorders. In recent years, altering inter-pulse-interval (IPI) regularly or irregularly in real time has emerged as a promising way to modulate the stimulation effects. However, algorithms to design IPI sequences are lacking. This study proposed a novel strategy to design pulse sequences with varying IPI based on immediate neuronal reactions. Firstly, to establish the correlationship between the neuronal reactions with varying IPIs, high-frequency stimulations with varying IPI in the range of 5–10 ms were applied at the alveus of the hippocampal CA1 region of anesthetized rats in vivo. Antidromically-evoked population spikes (APS) following each IPI were recorded and used as a biomarker to evaluate neuronal reactions to each pulse. A linear mapping model was established to estimate the varied APS amplitudes by the two preceding IPIs. Secondly, the mapping model was used to derive an algorithm for designing an IPI sequence that would be applied for generating a desired neuronal reaction pre-defined by a particular APS distribution. Finally, examples of stimulations with different IPI sequences designed by the algorithm were verified by rat experiments. The results showed that the designed IPI sequences were able to reproduce the desired APS responses of different distributions in the hippocampal stimulations. The novel algorithm of IPI design provides a potential way to obtain various stimulation effects for brain stimulation therapies. [ABSTRACT FROM AUTHOR]