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Background: Acoustic resolution-based photoacoustic endoscopy (ARPAE) is a non-invasive potential tool for imaging gastrointestinal and urogenital tracts. However, current ARPAE systems usually only provide 2D sectorial B-mode images, and have the limitation of the image quality significantly deteriorating out-of-focus regions due to transducers with fixed focus in these systems. To overcome these limitations, we put forward a modified back-projection method that can provide 3D images with dynamic focusing in ARPAE.Methods: A graphics processing unit (GPU)-based parallel computation technique was adopted for efficient computation. Both simulated and phantom/ex-vivo experiments were conducted to validate our method.Results: The findings indicated that our proposed method can effectively improve the lateral resolution and signal-to-noise ratio (SNR) in the out-of-focus regions. For a target 3 mm from the transducer focus, the new method can improve 11 times in the lateral resolution, along with an improvement of up to 37 dB in the SNR.Conclusions: 3D ARPAE provides high-quality imaging in both focus and out-of-focus regions.