Proton therapy is a type of radiation therapy that can provide better dose distribution compared to photon therapy by delivering most of the energy at the end of range, which is called the Bragg peak (BP). The protoacoustic technique was developed to determine the BP locations in vivo, but it requires a large dose delivery to the tissue to obtain a high number of signal averaging (NSA) to achieve a sufficient signal-to-noise ratio (SNR), which is not suitable for clinical use. A novel deep learning-based technique has been proposed to denoise acoustic signals and reduce BP range uncertainty with much lower doses. Three accelerometers were placed on the distal surface of a cylindrical polyethylene (PE) phantom to collect protoacoustic signals. In total, 512 raw signals were collected at each device. Device-specific stack autoencoder (SAE) denoising models were trained to denoise the noise-containing input signals, which were generated by averaging only 1, 2, 4, 8, 16, or 24 raw signals(low NSA signals), while the cleansignals were obtained by averaging 192 raw signals (high NSA). Both supervised and unsupervised training strategies were employed, and the evaluation of the models was based on mean squared error (MSE), SNR, and BP range uncertainty. Overall, the supervised SAEs outperformed the unsupervised SAEs in BP range verification. For the high accuracy detector, it achieved a BP range uncertainty of 0.20 ± 3.44 mm by averaging over 8 raw signals, while for the other two low accuracy detectors, they achieved the BP uncertainty of 1.44 ± 6.45 mm and -0.23 ± 4.88 mm by averaging 16 raw signals, respectively. This deep learning-based denoising method has shown promising results in enhancing the SNR of protoacoustic measurements and improving the accuracy in BP range verification. It greatly reduces the dose and time for potential clinical applications.