In this paper, the Deep Long-short term memory Autoencoder (DLAE), a regularized deep learning model, is proposed for the automatic severity assessment of phonological deviations which are crucial stuttering markers in children. This automatic noninvasive severity assessment plays a paramount role in prevenient diagnosis, progress inference, and post-care for the patients with specific speech disorder. The proposed model is an implementation of a multi-layered Autoencoder in the Encoder–Decoder architecture of the Long-Short Term Memory (LSTM) model with hierarchically appended hidden layers and hidden units. The DLAE has definite advantage over the baseline Autoencoders. During the training phase, the proposed DLAE reconstructs the phonological features in an unsupervised fashion and the latent bottleneck features are extracted from the Encoder. The trained and regularized DLAE model with drop out is then used to predict the severity of the phonological deviation with high precision and classification accuracy compared to the baseline models.