Automatic segmentation of the prostate peripheral zone on Magnetic Resonance Images (MRI) is a necessary but challenging step for accurate prostate cancer diagnosis. Deep learning (DL) based methods, such as U-Net, have recently been developed to segment the prostate and its' sub-regions. Nevertheless, the presence of class imbalance in the image labels, where the background pixels dominate over the region to be segmented, may severely hamper the segmentation performance. In the present work, we propose a DL-based preprocessing pipeline for segmenting the peripheral zone of the prostate by cropping unnecessary information without making a priori assumptions regarding the location of the region of interest. The effect of DL-cropping for improving the segmentation performance was compared to the standard center-cropping using three state-of-the-art DL networks, namely U-net, Bridged U-net and Dense U-net. The proposed method achieved an improvement of 24%, 12% and 15% for the U-net, Bridged U-net and Dense U-net, respectively, in terms of Dice score.