For the safe and reliable operation of battery-driven machines, accurate state-of-charge (SOC) estimations are necessary. Unfortunately, existing methods often fail to identify patterns relevant to long-term SOC estimation due to complex battery cell characteristics such as aging. In this paper, we propose the Uncorrelated Sparse Autoencoder with Long Short-Term Memory (USAL). USAL is a novel neural network that addresses the challenging task of long-term SOC estimation given a limited initial history of a cell’s charge-discharge behavior. USAL uses a multi-task learning strategy to harness the advantages of sparse autoencoders and Long Short-term Memory (LSTM) networks by enforcing correlation penalties. The USAL simultaneously learns to (i) generate a latent space of informative SOC encodings from commonly measured cell characteristics, (ii) penalize for high multicollinearity between encodings, and (iii) identify non-trivial long and short temporal correlations between the encodings using LSTM cells. USAL outperforms benchmarked models in our experiments when trained on five initial charge-discharge cycles across multiple battery cells using three publicly available accelerated aging datasets. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This paper proposes USAL, a custom-built deep neural network to address the challenging task of long-term SOC estimations in battery cells. Long-term SOC estimation involves estimating SOC for cycles near End-Of-Life (EOL) given some initial charge-discharge cycles. Three fundamental steps involved in long-term SOC estimations using USAL are (i) exploiting a multi-task learning strategy to learn efficient encodings given limited training data, (ii) penalizing these encodings for high correlations to efficiently transform measured inputs into a space of informative features, and (iii) mapping of aging-related trends to support long-term SOC estimations. USAL is designed to be a data-driven SOC estimation method that is (i) capable of alerting the user to a faulty cell when integrated into a real-life Battery Management System (BMS) and (ii) identifying the relative quality of a battery cell from only a few initial charge-discharge cycles.