Advancement in digital pathology has enabled deep learning-based computer vision techniques for automated diagnosis and prognosis of diseases. The essentiality of early detection and prognosis of any cancer category lies in the fact that it can speed up the subsequent medical treatment procedures of patients. About 10% of all cancer cases worldwide are related to colorectal cancer (CRC), and it is also the third most common category of cancer (Egeblad et al. in Dev Cell 18:884–901, 2010). So, it is clinically important to classify and make an objective evaluation of colorectal cancer histological images. The classification performance of current methodologies primarily relies on the use of various combinations of texture-based features and classifiers or transfer learning to classify different organisational kinds. As a result of the diversity of tissue types and characteristics present in histological images, classification is still a challenging task. In this study, we have put forth a novel and effective stacking (Wolpert in Neural Netw 5:241–59, 1992) ensemble (Zhang and Yunqian (eds) Ensemble machine learning: methods and applications. Springer Science; Business Media, 2012) technique for classification on the histopathological image analysis benchmark dataset Kather-5 K (Kather et al. in Sci Rep 6:27988, 2016). The ensemble consists of two cutting-edge deep learning architectures, ResNet18 (He et al. in Proceedings of the IEEE conference on computer vision and pattern recognition 2016, pp 770–778) and EfficientNetB0 (Tan and Le Efficientnet: rethinking model scaling for convolutional neural networks. International conference on machine learning 2019 May 24. PMLR, pp 6105–6114), acting as weak learners, and an ANN acting as the meta-learner. The proposed approach obtained a remarkable accuracy of 97.20% in CRC classification on the said dataset.