Accurate state of charge (SOC) estimation of lithium-ion (Li-ion) batteries is crucial in prolonging cell lifespan and ensuring its safe operation for electric vehicle applications. In this article, we propose the deep learning-based transformer model trained with self-supervised learning (SSL) for end-to-end SOC estimation without the requirements of feature engineering or adaptive filtering. We demonstrate that with the SSL framework, the proposed deep learning transformer model achieves the lowest root-mean-square-error (RMSE) of 0.90% and a mean-absolute-error (MAE) of 0.44% at constant ambient temperature, and RMSE of 1.19% and a MAE of 0.7% at varying ambient temperature. With SSL, the proposed model can be trained with as few as 5 epochs using only 20% of the total training data and still achieves less than 1.9% RMSE on the test data. Finally, we also demonstrate that the learning weights during the SSL training can be transferred to a new Li-ion cell with different chemistry and still achieve on-par performance compared to the models trained from scratch on the new cell.