In clinical examination, event-related potentials (ERPs) are estimated by averaging across multiple responses, which suppresses background EEG. However, acquiring the number of responses needed for this process is time consuming. We therefore propose a method for shortening the measurement time using weighted-average processing based on the output of deep learning. Using P300 as a representative component, here we focused on the shape of the ERP and evaluated whether our method emphasizes the P300 peak amplitude more than conventional averaging, while still maintaining the waveform shape and the P300 peak latency. Thus, using either CNN or EEGNet, the correlation coefficient reflecting the waveform shape, the peak P300 amplitude, and the peak latency were evaluated and compared with the same factors obtained from conventional waveform averaging. Additionally, the degree of background EEG suppression provided by our method was evaluated using the root mean square of the pre-stimulation waveform, and the number of fewer responses required for averaging (i.e., the reduction in measurement time) was calculated.The results showed that compared with P300 values obtained through conventional averaging, our method allowed for the same shape and response latency, but with a higher amplitude, while requiring a smaller number of responses. Our method showed that by using EEGNet, measurement time could be reduced by 13.7%. This corresponds to approximately a 40-second reduction for every 5 minutes of measurement time.