Denoising of Computed tomography (CT) images is a critical aspect of image processing that is expected to improve the performance of Computer‐aided diagnosis (CAD) systems. However, the use of complex imaging modalities such as CT imaging to ascertain pancreatic cancer is vulnerable to gaussian and poisson noises, making image denoising an imperative step for the accurate performance of CAD systems. This paper presents a Bilateral median based autoencoder network (BMAuto‐Net) constructed with intermediate batch normalization layers and dropout factors to eliminate gaussian noise from the CT images. The skip connections adjoining the network, prevent performance degradation that generally occurs in most autoencoder architectures. Based on the presented study, BMAuto‐Net is reckoned to outperform other traditional filters and autoencoders. The performance measurement of the proposed architecture is performed using the peak signal‐to‐noise ratio (PSNR), mean squared error (MSE), and structured similarity index (SSIM) metric values. The Cancer imaging archive (TCIA) dataset consisting of 19 000 CT images is used to validate the performance of the architecture with average PSNR values of 30.01, 30.53, and 30.52, MSE values of 98.23, 98.87, and 98.94, and SSIM of values of 0.67, 0.60, and 0.57 for noise factors (NFs) of 0.1, 0.3, and 0.5 respectively.