This research work develops new and better prognostic markers for predicting Childhood MedulloBlastoma (CMB) using a well-defined deep learning architecture. A deep learning architecture could be designed using ideas from image processing and neural networks to predict CMB using histopathological images. First, a convolution process transforms the histopathological image into deep features that uniquely describe it using different two-dimensional filters of various sizes. A 10-layer deep learning architecture is designed to extract deep features. The introduction of pooling layers in the architecture reduces the feature dimension. The extracted and dimension-reduced deep features from the arrangement of convolution layers and pooling layers are used to classify histopathological images using a neural network classifier. The performance of the CMB classification system is evaluated using 1414 (10× magnification) and 1071 (100× magnification) augmented histopathological images with five classes of CMB such as desmoplastic, nodular, large cell, classic, and normal. Experimental results show that the average classification accuracy of 99.38% (10×) and 99.07% (100×) is attained by the proposed CNB classification system.