Conventional noninvasive electroencephalogram (EEG) suffers from poor spatial resolution due to the effect of volume conductor. Based on acoustoelectric (AE) effect, acoustoelectric brain imaging (ABI) is a novel neuroimaging technique for mapping brain electrical activity, which is potential of high resolution in both space and time domains. This study proposes a source signal modulation mechanism with pulse focused ultrasound (pFU) for ABI. First, spectral analysis of AE signal is implemented at different pulse repetition frequencies (PRF), including 100Hz, 200Hz, 500Hz and 1kHz. Results of amplitude spectrum indicate that obvious high amplitude response of AE signal is observed at each PRF and corresponding harmonic frequencies. Besides, the modulation relationship between AE signal and PRF is investigated in detail. For each source signal of 10Hz and 30Hz, the oscillation frequency of AE signal is consistent with the corresponding PRF. What’s more, for different PRFs, the envelope of AE signal is of the same frequency and phase with the source signal. These experiment results demonstrate that pulse focused ultrasound has a modulation mechanism on source signal at PRF and confirm the feasibility of restoring source signal from the modulated AE signal.