Lung cancer is the deadliest cancer in the world. It is caused by unchecked cell division of damaged cells in the lungs forming tumors that eventually prevent the lung from functioning properly. Identification of novel unsupervised subtypes of lung cancer is critical to reveal new insights into the underlying biology of cancer and ensure that patients receive specialized precision treatment based on the subtype of cancer they are suffering from. The ability of modern sequencing tools to produce patient-specific RNA sequencing (RNA-seq) gene expression data has transformed cancer research by offering in-depth understanding of the molecular landscape of cancer. This paper reports on a pipeline that comprise of a Deep Autoencoder (DAE) model coupled with hierarchical agglomerative clustering (H-Clust). It aims to identify new unsupervised lung cancer subtypes from RNA-seq expression samples collected from a publicly available dataset. Further, a deep learning (DL) model, Artificial Neural Network (ANN) is used to classify a patient’s data into one of the newly identified subtypes.