Simultaneous point-by-point raster scanning of optical and acoustic beams has been widely adapted to high-speed photoacoustic microscopy (PAM) using a water-immersible microelectromechanical system or galvanometer scanner. However, when using high-speed water-immersible scanners, the two consecutively acquired bidirectional PAM images are misaligned with each other because of unstable performance, which causes a non-uniform time interval between scanning points. Therefore, only one unidirectionally acquired image is typically used; consequently, the imaging speed is reduced by half. Here, we demonstrate a scanning framework based on a deep neural network (DNN) to correct misaligned PAM images acquired via bidirectional raster scanning. The proposed method doubles the imaging speed compared to that of conventional methods by aligning nonlinear mismatched cross-sectional B-scan photoacoustic images during bidirectional raster scanning. Our DNN-assisted raster scanning framework can further potentially be applied to other raster scanning-based biomedical imaging tools, such as optical coherence tomography, ultrasound microscopy, and confocal microscopy.